mosdepth
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Published
20 hours ago •
brentp
brentp
N region?
Hi, I found depth and coverage contain N region,why use reference? chr1 0 10001 1 0.01 for hg19,chr1:0-1000 is N. average depth= total depth/region size .The region size contains n, so I think it's incorrect to calculate the depth。
can you show the output of samtools view $bam chr1:1-10000 for the bam in question?
can you show the output of
samtools view $bam chr1:1-10000for the bam in question? my reference is hg19
E100001798L1C004R0250660061 129 chr1 9999 0 63S81M chrY 59363140 0 CACTATGGTGACTAACCAGAAATGGGCATTCTGTAAATGCTAGATACAAAATAAATAAATAAGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT EEEEEEEEEDEEEEFEEEEFEEEEDEEEFDEEEEEFEEEEEEEFEEEEEEFEDFEEEFEBEEEEFEEEEEDFEEEEDEEEECEEFEEEEEEEEEEEFEEEEEEEEEEEEEEEEEEEECEEEEEEEEEEEDEEEEE=EEEEE7EE NM:i:0 MD:Z:81 MC:Z:144M AS:i:81 XS:i:79 RG:Z:NA12878bgi SA:Z:chr13,26286178,-,79S65M,0,0;
E100001798L1C004R0302388074 65 chr1 9999 0 55S66M23S chr6 93812543 0 ATATCCCCCAAGTATGAGTTGCCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACAC E=E9EDCCEEC==EEDA8BEEEDEEEBEEE@EEEEBCCE6EEEEEEEEDEEDEECD?CD>AEEEDCBDDEECDDEEEDEEEEDDCEE<E@DC@D4EDEEED>CDDD>BDEEEDBEEEEEDEE@DB=DDEEDDDDEABD>@EDD9 NM:i:0 MD:Z:66 MC:Z:138M AS:i:66 XS:i:65 RG:Z:NA12878bgi SA:Z:chr5,18606943,-,80S64M,0,0;
E100001798L1C030R0022748976 129 chr1 9999 0 50S94M chrX 155260132 0 ACTCAGGCCTCTCTCCCTCTTGTCATGAAGCCACCCAGCCCCACTCCTATGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA EEEEEE9CEDDEEEEEEEEEEEEEEEEEEAEEEEDEEBEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDEEEEEEEEEEEDEEEEEBEEEEEEEEEDEECEEEEEEDEEEDBCEEEDEDDE@DEEEEBDCEE NM:i:0 MD:Z:94 MC:Z:144M AS:i:94 XS:i:92 RG:Z:NA12878bgi SA:Z:chr13,93649045,-,86S58M,0,0;
E100001798L1C030R0022748977 129 chr1 9999 0 50S94M chrX 155260132 0 ACTCAGGCCTCTCTCCCTCTTGTCATGAAGCCACCCAGCCCCACTCCTATGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA EEEEFE?EEEEEEEEEEEEEEE@EEEEEE@EEEEEEEDEDEEEEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDEEFEEEEEEEEEEEECEEEEEDEEEEEDEEEEEEEEEDEEEEEEEEECEEDEEECBEEDEEEE NM:i:0 MD:Z:94 MC:Z:144M AS:i:94 XS:i:92 RG:Z:NA12878bgi SA:Z:chr13,93649045,-,86S58M,0,0;
E100001798L1C002R0360190636 177 chr1 9999 0 78S54M chr3 196625626 0 ACAGACCGGAATGGAATCCACACCGAATGGAATCGAATGGTATCAACACCAACCGGAAAAAAACGGAATTATCGAATGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC @.DB?&-)/&?2E2;E%8(6D8'>&.EEB:C@+E.C=DA<2E5AE'7BEAE8,CEECECE;@EEEE:>ED@5C2BEDE<CCBDDEE@@/E@<EB=<D9E7AEEEB;EDBDE4CDEE?BEC+C@E?DEEE<DE NM:i:0 MD:Z:54 MC:Z:144M AS:i:54 XS:i:52 RG:Z:NA12878bgi
E100001798L1C010R0101530106 177 chr1 9999 0 62S82M chr4 39901775 0 ATAATTAGAATTAAATTTTGAGATAAAATTACATTAAACATCATATTTCTTTTTCACTGCATGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA DDDB?ED<EDBAEEAECDE@ECEEEEDDEE?DDEDED;DCEE9E6DDEEE?;E@;BEAB:CEEEEC-9?EEDBC8CEA?EBDEEED;EEDDB5EEDDBBDEDE@@DEDEEDCEEEC?CEEE;DCFEEDDEEEDECEECDDBEEE NM:i:0 MD:Z:82 MC:Z:144M AS:i:82 XS:i:80 RG:Z:NA12878bgi SA:Z:chr4,39901713,+,79S65M,0,0;
E100001798L1C020R0281503335 113 chr1 9999 0 40S66M38S chr5 18606943 0 GAGTTGCCTAGACCAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAG ;E)@CE%ECAE@'E3@:-DDC;DDEE4CE?=@CCC:>8D=E?EBCCD?EB;E+DD3DDEEE=,;?EDDD2C@ED@CBDD@C7A<DA>@EEEDD5=EEBCECBEEDDEEEBEEE@DEEEEEEECE<AEDC@EBDEEEECD?EEEE NM:i:0 MD:Z:66 MC:Z:34S110M AS:i:66 XS:i:65 RG:Z:NA12878bgi SA:Z:chr5,18606943,+,95S49M,0,1;chr5,18606896,+,40M104S,0,0;
E100001798L1C003R0210035048 161 chr1 10000 0 68S76M chr5 10005 0 AACAAATTTGAAAACTTAGATGAAATGAACAAATTCCTTGAAAGACACATAATACCAAAGCTCACACAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA EEEAFCEFEEEEEFEFEBEEEEDEEEEEEFEEEDFDFFFEEFEEFEDFEEEEEEEEEEEEEEFEEEFEEEEEFEEEEFEEEFEEFEEEEEEFFFEEEEEEEFFEFEEEFEEEEEEEFFEEEEEEEEEFEEEEFEEEEEFEEEEC NM:i:0 MD:Z:76 MC:Z:144M AS:i:76 XS:i:75 RG:Z:NA12878bgi SA:Z:chr3,137998590,-,75S69M,0,0;
E100001798L1C005R0040703221 163 chr1 10000 44 8M1D47M1D89M = 10053 197 CTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA EEEEEDEEEEEE8EEEEEFEDAEDEDEEEEEEE@CDEEEEEEEEEEEEEEEEAEEE8EEEE?@EEEDEEEEEE?F>EEEED<EDEEE9E@EECEEEEDDEEAABCFECEBEDEE@DEDEE?C9DEDEECC>DDBEEEEEEEEEA NM:i:3 MD:Z:0A7^A47^A89 MC:Z:3M1D121M1I19M AS:i:129 XS:i:121 RG:Z:NA12878bgi XA:Z:chr4,-191044073,21M3D16M1D98M1D9M,5;chr1,-249240087,13M1I19M4I12M1D95M,6;chr4,+10059,8M1D97M1D32M7S,4;chr18,+10040,8M1D29M1I69M2D11M1D26M,5;chr15,-102521204,2S12M1D6M1D6M1D11M1D98M1D9M,5;
E100001798L1C011R0220896181 129 chr1 10000 0 41S103M chr12 133841747 0 TTGGGGGGTTGGGGGCTGGGGGAGGGNTAGCATTAGGAGAAATAANCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCNTAACCC EAEEEEEEEEEEEEEEEEEEEEEEDE!DEDEEEEEEDEEEEEEEE!EEEEEEEEEEEEEEEEDEDEDEEEDEEEEEEEEEEDEEEEEEEEEEEDEEDEEEEEEEEDEEEEEEAEEEDEAEEEDDEECECDEDEEBEE!6DEEEE NM:i:2 MD:Z:4C91C6 MC:Z:144M AS:i:99 XS:i:98 RG:Z:NA12878bgi SA:Z:chr3,158703507,-,99S45M,0,1;
E100001798L1C014R0122786484 129 chr1 10000 0 54S90M chr12 133841650 0 GGCCTTTCATGAGAGGGGGATTGGTTTCATGACTCTCAATTTTGGAAGAATAGAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC FEDEFFEECEE<EDFEEEFEEEEEEEEE@EEEEDEFEEDDEFFDEE8EE>ECEEDEEEFEEEEDDEEEDFDEEEEEDEEEAEEEEEEEEEEEEEEEEEDEEEEEDEEEECEEEEDEEEEEEDEEDEDEEEEEEDDEDEEEDEED NM:i:0 MD:Z:90 MC:Z:119M25S AS:i:90 XS:i:89 RG:Z:NA12878bgi SA:Z:chr6,90069548,+,62M82S,0,0;
E100001798L1C014R0161139420 129 chr1 10000 0 64S80M chrX 155260133 0 GCGCTTAGCAACACTTAACATTAGAAAGCTCTGTCTCTGTGTGTCCCTAGCTTTTAAATGGGTAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT :??@EEE1CEE7E6DEEEDEC>EDEEED@E?EECCDDE@B;EDEA8BEE=@EEEDEEEEE8DDEEEEE?=CDEEC8CEED4CCEEE3C8EEEDBCEECD@BEEEEBBDED?DBEECB>@EBEDDEEE@*@1DDC;<<DE7C=CC NM:i:0 MD:Z:80 MC:Z:144M AS:i:80 XS:i:79 RG:Z:NA12878bgi SA:Z:chr2,217192307,+,70M74S,0,0;
E100001798L1C037R0173130374 161 chr1 10000 9 8M1D59M1D77M chr5 11715 0 CTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA EED=EDEFAEEDEDCEE:ECCEEEEDEEEEEEEEEDEDEEEEE@?EECDDEEEECEDEEEECAEEE?<EEE=EEEEEC4EEEE@8EDEEE@AEEE@?@EEF::DEEEB=DFECCEEEEAEBEEE?CCEDE7DEEEE8BCEEE>E NM:i:4 MD:Z:0A7^A52T6^A77 MC:Z:9M1D80M55S AS:i:124 XS:i:118 RG:Z:NA12878bgi XA:Z:chr5,+11633,8M1D59M1D40M1D37M,4;chr15,-102521231,14S23M1D98M1D9M,4;chr1,-249240093,7M1I18M1D11M2D86M1I11M1D9M,7;
E100001798L1C040R0231695919 161 chr1 10000 0 53S91M chr5 10031 0 CTTTTTCTTCCTTGCCCAAATTCTTATCTAAGGGGCCTAGGGAGTTATGCTCTATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 8EEEEFBEECEE@;DEBEEEFEEEE>D>E9E'@-1E@FE,+?E9EEEE=EEEFECECDEBEDDEBAFCEEDEEEECEEEEEEEDDEDEEEEEEEEEDBEEEDEEEEEEEEEEEDFEEDEEEE?EEEEEEFEEEEEFFE@CEEEE NM:i:0 MD:Z:91 MC:Z:25S119M AS:i:91 XS:i:90 RG:Z:NA12878bgi SA:Z:chrX,1745532,-,86S58M,0,0;
E100001798L1C006R0133394652 177 chr1 10000 0 40S104M chr16 21574411 0 CAGTTATGAAGGCTGGGAAGTCTGAGATCAGGGTGCCAGCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT CDE?A>CCEE=7E<D0ACE<EDBBE<?EEE?E;EC.>EBD.ECBBEEE;@=D>EEDEDECB3B2EE7=@=EEE?EDEEE.D=DECBDEEEA9/<EDE4E2EECB@=DFC>3?DEAE9?5EBEE?=E<E4C;EDCCCEED4CADE NM:i:0 MD:Z:104 MC:Z:144M AS:i:104 XS:i:103 RG:Z:NA12878bgi SA:Z:chr16,21574374,+,102S42M,0,0;
E100001798L1C011R0253875369 113 chr1 10000 0 42S102M chr4 169634121 0 AGAGAGAAAAGAGTAGGCTAGTCAATGCTAGGGAAATAAAGAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC EEEEEDEEEEEEEEEEEEDEE;EDEEEDEEDAAEEDA<EEEEEEEDEECEEDEDEEDDDEEEECEEEEECEEEEEEEEEEECEEEEEEEEEEBCEEEEEDEEDDDEEEEECEDEEEEDEEEEEEDEAEEEEEEEEECCEEAEBE NM:i:0 MD:Z:102 MC:Z:144M AS:i:102 XS:i:101 RG:Z:NA12878bgi SA:Z:chr4,169633988,+,95S49M,0,0;
E100001798L1C011R0352187011 145 chr1 10000 0 52S92M = 91243122 91233032 ATTTCTGCTGAGTGTCTCCAAGATGCCTCAGACATCTCTGGGTACTTTTTGCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT :C;EDCDDAEECEE<E<CEEEDAE?@EDAED?E<EEEEECEEECEEEE=ECEECEDEDEEBEEEEE?>EDEEDAEEEECDEEDEDCEEEEEDECEEEBEBEEECDEEEA?EEEECDEDEEDDDDEEEDDDEFEEEDEEDEEDEE NM:i:0 MD:Z:92 MC:Z:144M AS:i:92 XS:i:91 RG:Z:NA12878bgi SA:Z:chr1,91243219,-,53M91S,0,0;
E100001798L1C015R0150427817 177 chr1 10000 0 61S83M chr5 103920743 0 AAGCAGCTGCCTTGATCCACTCTAGAAAAATGTTCAGAGTCTATGTTTCCTGTTGACACCCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC EEDED>ADEEEDE@E9EEDEEEEEDEEEE>ECDEEE=EEEEEEEEEEEDEFEEECAECEBEEEEEEDEECEEEEEECAEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEBEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NM:i:0 MD:Z:83 MC:Z:58S86M AS:i:83 XS:i:82 RG:Z:NA12878bgi SA:Z:chr5,103920743,+,80S64M,0,0;
E100001798L1C018R0293069090 81 chr1 10000 0 36S108M = 49680058 49669952 TTTTACACACCATCTGCTGGTAGACTGAGACTAGTAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC DEEEBEEEEDEDDDEE=DDEDEDDEEEE<BDEEDEEEE@EBCECEDEDDEDD=ECCDEAECEECEDCEEEEEEE8EEADEEEC<DEEDDE?EEED?EEEECDEEEEDDEEEEEEEEEEECEEEDAAEEEE@CDECDABCEED@D NM:i:0 MD:Z:108 MC:Z:144M AS:i:108 XS:i:107 RG:Z:NA12878bgi SA:Z:chr1,49680389,-,40M104S,0,0;
E100001798L1C022R0062456443 145 chr1 10000 0 51S93M chr7 131105024 0 GAGAAGTGTGAGAAAAAGAAGCTAAGGATGACTTAAAGTTTTGACCTGAGCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ?EDEEED?5EEADEEEEEEE?>EEECD?D@EDDEEEEEEDEEA;;EEEEE7DEDEECEEE?=CDEC>8DEEEA?@EEE?A9AEEEE:>EEEEECEEECEDEEB?<EEEEEAAFEDCD?EEEE2EEEEEC;FEEE@EEECAABEE NM:i:0 MD:Z:93 MC:Z:144M AS:i:93 XS:i:92 RG:Z:NA12878bgi SA:Z:chr7,131105139,-,52M92S,0,0;
E100001798L1C027R0320878876 121 chr1 10000 0 79S65M = 10000 0 CTGGTTTATAGCATCGCGAATTTTGACTGCAATATTTCCTCCAGAAAGAGTGACATCTTGTCCTGTGATAAAATCGCTCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC BEEEEDECFEE3DEEEEEEEEEEEEEEEEDEEEEEBECECEEEEEEEEFEE<EEEEEEECEEEEEEEFEEEEEEE;EFEEEDEDEEEEECEEEEEEEEFEDAEEEEEEEEEEEEEEEEEE?EEDEEDEEEBE9DEEEDEEEEEE NM:i:0 MD:Z:65 AS:i:65 XS:i:64 RG:Z:NA12878bgi
E100001798L1C027R0320878876 181 chr1 10000 0 * = 10000 0 CTTTATGGAATGCCCTCCCAACATCTGGTAGACAATCCTCCAGGGACGATTTAATCCCAGCCGCCGTGCAGGCCTTAACCACGGCCCACAACTTATGTCTGGGTGTTATTCCAGGTGAGACCTCACACAAGGACACACCCGAGT EECEEEBAEDEDE@ECEBEEDEEEEEEEEEEEEEEEDEEAEEEEEAEFEEEEBBDECEE9DEEEEEEEEEEEEEEEEEEEEEEEEAE?EE9DECEFEFCEEEEEEEEEEEEEEEEEEEEDECEEEEEEEEEEEEEEEEEEEEEE MC:Z:79S65M AS:i:0 XS:i:0 RG:Z:NA12878bgi
E100001798L1C028R0391082482 81 chr1 10000 0 52S58M1I33M chr6 68720281 0 ATTAGAGTCAGAGATAGAGAAGTACATACAAAAACAGGGGTGTGTGTGAGAAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCC EEEEEEE0BEEECCEEEFEEEEEE*EEEEEDEEDDEDECEC?EDEBEDE<DDEEEDEDEEEEDEEE=DEEEEDCDDDECDCEEEEBCEEECEEEEEEEECDEEECEEEEECEEEEDEEAEEED:EEEEE*DEEE8D3DEE@E:E NM:i:1 MD:Z:91 MC:Z:144M AS:i:84 XS:i:83 RG:Z:NA12878bgi SA:Z:chr6,68720548,-,51M93S,0,0;
E100001798L1C037R0332432346 145 chr1 10000 0 60S84M chr3 82016368 0 AAAACCCTGGAAGCAGAAGAGAGACACTGAGAAGAGAGAAGATTCTTCCTTTTTCCAGGAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC D*EDBAE9A/[email protected]'A;2E98EEDE>=:@E:7/E-CE8DEDEEE2ED@DE>EDCDE/E@;EEC/DEEDD?7@EEA8@DDE:<@@EEEAEDCEA@E,CEBDE=@EE1D:ADEDE1EEEDDD@EEEE@EEECDE?EDDE8 NM:i:0 MD:Z:84 MC:Z:144M AS:i:84 XS:i:83 RG:Z:NA12878bgi SA:Z:chr3,82016452,-,68M76S,0,0;
mosdepth just reports the coverage as it is, without considering the reference bases.