BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716306.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,523,752 number of mapped reads = 1,408,462 (92.43%) number of supplementary alignments = 27,878 (1.83%) number of secondary alignments = 0 number of mapped bases = 112,034,783 bp number of sequenced bases = 111,982,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,076 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6533 >>>>>>> ACTG content number of A's = 28,688,772 bp (25.62%) number of C's = 21,857,203 bp (19.52%) number of T's = 34,507,622 bp (30.82%) number of G's = 26,921,050 bp (24.04%) number of N's = 8,132 bp (0.01%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 724,534 number of insertions = 8,759 mapped reads with insertion percentage = 0.61% number of deletions = 26,851 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.322X There is a 3.18% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 9079781 0.0364283184674593 0.5818563526466561 chr2 243199373 9427773 0.038765613922861555 0.3705166976854516 chr3 198022430 7368365 0.03720974942081056 0.21135648433141258 chr4 191154276 7330352 0.0383478316749765 0.27976235130328964 chr5 180915260 6700815 0.03703841787586078 0.21252615405439504 chr6 171115067 6303238 0.0368362535836777 0.22701731334594613 chr7 159138663 6125548 0.038491890559618436 0.4000378183593667 chr8 146364022 5835986 0.039873091216364634 0.3962429762189969 chr9 141213431 4694871 0.03324663218472469 0.2840404192967172 chr10 135534747 5368088 0.03960672904048731 0.35765992931285606 chr11 135006516 5143865 0.03810086470196742 0.3038546967751981 chr12 133851895 4987057 0.03725802313071473 0.21340768352556497 chr13 115169878 3602325 0.03127836082278389 0.1953570985568882 chr14 107349540 3367846 0.03137271012060229 0.2063260978032252 chr15 102531392 3234421 0.03154566554602126 0.1951983515528884 chr16 90354753 3269331 0.03618327637949494 0.22436049445504633 chr17 81195210 3080464 0.03793898679491069 0.2386773733347708 chr18 78077248 3006074 0.0385012801680715 0.4548155426433112 chr19 59128983 2256632 0.03816456643605726 0.3851521178280841 chr20 63025520 2428618 0.038533882782720394 0.2267245974785631 chr21 48129895 1487130 0.030898259802976922 0.22653113770771927 chr22 51304566 1318521 0.025699876303407383 0.1776161544315758 chrMT 16571 16841 1.0162935248325389 1.1430932382422712 chrX 155270560 6245603 0.04022399996496438 0.24756265989871373 chrY 59373566 355238 0.0059831002907927075 0.21521168213166209