bwa mem -a output all alignments for SE or unpaired PE

[fanshu1986]

-a means output all alignments for SE or unpaired PE, I find there is a bug two different ref, first is only a genome A, but second is thousands genomes including A, some reads can map first ,but can't map A of second

first NB501248AR:475:HT25HBGXH:1:11101:11813:4458 16 59_01B.CN.2012.12CN.YNKM200199.KJ484435 4063 60 75M * 0 0 AAAATTTTCGGGTTTATTACAGGGACAGCAGAGAACCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAAGGTG E/E6EAEEEEAEAE/EEEEEEE<EEEEEEEEEAEEEAEEEEEEEEEEEEEEA<EEEEEEEEAAEEEEEEEAAAAA NM:i:1 MD:Z:34C40 AS:i:70 XS:i:10

second @SQ SN:59_01B.CN.2012.12CN.YNKM200199.KJ484435 LN:8751

NB501248AR:475:HT25HBGXH:1:11101:11813:4458 16 77_cpx.MY.2014.14MYNBB090.KX673820 4134 5 75M * 0 0 AAAATTTTCGGGTTTATTACAGGGACAGCAGAGAACCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAAGGTG E/E6EAEEEEAEAE/EEEEEEE<EEEEEEEEEAEEEAEEEEEEEEEEEEEEA<EEEEEEEEAAEEEEEEEAAAAA NM:i:0 MD:Z:75 AS:i:75 XS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 01_AE.CN.2007.GX070044.JX112833 4184 0 75M * 0 0 * * NM:i:1 MD:Z:4C70 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 A6.RU.2012.IRK028.MH330361 4255 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 75_BF1.IT.2001.53143.GU595149 4196 0 75M * 0 0 * * NM:i:1 MD:Z:64G10 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 G.NG.2009.09NG010157.KX389631 4094 0 75M * 0 0 * * NM:i:1 MD:Z:18T56 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 A6.RU.2016.RU_ERS_1019_2016.MT334926 4182 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 A6.RU.2016.RU_ERS_1032_2016.MT369951 4184 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 A6.RU.2016.RU_ERS_1018_2016.MT334925 4178 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 A6.RU.2016.RU_ERS_1042_2016.MT369961 4184 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70 NB501248AR:475:HT25HBGXH:1:11101:11813:4458 272 43_02G.SA.2003.J11456.EU697909 4416 0 75M * 0 0 * * NM:i:1 MD:Z:22A52 AS:i:70