BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971299.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 10,241,900 number of mapped reads = 8,659,048 (84.55%) number of secondary alignments = 0 number of mapped bases = 340,409,475 bp number of sequenced bases = 340,374,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,450,953 duplication rate = 15.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.7081 >>>>>>> ACTG content number of A's = 96,250,295 bp (28.28%) number of C's = 71,227,500 bp (20.93%) number of T's = 99,521,418 bp (29.24%) number of G's = 73,373,068 bp (21.56%) number of N's = 2,616 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,148,009 number of insertions = 13,888 mapped reads with insertion percentage = 0.16% number of deletions = 28,116 mapped reads with deletion percentage = 0.32% homopolymer indels = 37.53% >>>>>>> Coverage mean coverageData = 0.11X std coverageData = 1.0481X There is a 7.76% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 30974225 0.12426939951335167 2.287306635882965 chr2 243199373 28732565 0.11814407514940427 0.8907704530416722 chr3 198022430 23108148 0.11669459868763352 0.46137173162745293 chr4 191154276 22455716 0.11747430646019134 0.4962242014129153 chr5 180915260 21215969 0.11727020152971065 0.4902691321461633 chr6 171115067 20130388 0.11764240492042702 0.59023347118805 chr7 159138663 19263092 0.12104595851732146 1.258010453300301 chr8 146364022 17569536 0.12003999179525143 1.7316102687314416 chr9 141213431 14386238 0.10187584777258192 0.8807409685128637 chr10 135534747 15939786 0.11760663853970968 0.91904774905059 chr11 135006516 15644215 0.11587748105432186 0.7527477483812184 chr12 133851895 15535943 0.116068158766075 0.4941187764000098 chr13 115169878 10939291 0.09498395926059763 0.40391491274168767 chr14 107349540 10398173 0.09686276252324882 0.526688893778423 chr15 102531392 9437322 0.09204324466793545 0.40137499606987365 chr16 90354753 9121385 0.10095080443637536 0.5031005995113851 chr17 81195210 8755096 0.10782774008466756 0.47885616584319085 chr18 78077248 9028945 0.11564117884892665 1.7244945535328233 chr19 59128983 7039675 0.11905625029945129 2.0539239887685206 chr20 63025520 6614187 0.1049445843524972 0.4922180688521125 chr21 48129895 4260431 0.08851943267277022 0.5035732133927018 chr22 51304566 3530220 0.06880908026782645 0.40646121077432185 chrMT 16571 49732 3.0011465813771045 3.236536283632121 chrX 155270560 13133301 0.08458332989846884 0.5652149784524407 chrY 59373566 3145896 0.05298479124531614 0.458972395781259