BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549011.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 = 11,426,869 number of mapped reads = 9,716,178 (85.03%) number of secondary alignments = 0 number of mapped bases = 384,537,979 bp number of sequenced bases = 384,499,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,010,648 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0369 >>>>>>> ACTG content number of A's = 114,246,347 bp (29.71%) number of C's = 77,819,981 bp (20.24%) number of T's = 114,864,475 bp (29.87%) number of G's = 77,553,872 bp (20.17%) number of N's = 14,687 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 925,294 number of insertions = 12,543 mapped reads with insertion percentage = 0.13% number of deletions = 29,559 mapped reads with deletion percentage = 0.3% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.1242X std coverageData = 2.7162X There is a 5.81% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 29572283 0.11864477160119091 1.3617445524608605 chr2 243199373 32357345 0.13304863660154256 0.8064617069543821 chr3 198022430 26262618 0.13262446077446882 0.6660616186053236 chr4 191154276 25699261 0.13444251176468583 0.6874727144539045 chr5 180915260 24098668 0.1332041752586266 0.6675398350570462 chr6 171115067 22632135 0.13226266626772265 0.6956437889124797 chr7 159138663 21161994 0.132978332235957 1.0156568303478875 chr8 146364022 21146914 0.1444816404402989 11.933783589387847 chr9 141213431 16094432 0.11397238836297377 0.742139827404149 chr10 135534747 17918843 0.1322084808259538 0.7864728247252435 chr11 135006516 17318182 0.12827663814389523 0.8618310229029061 chr12 133851895 17287635 0.12915495144839004 0.6637921938034149 chr13 115169878 12633994 0.10969877036771715 0.6022162454084519 chr14 107349540 11742781 0.10938827497537483 0.6674483576370479 chr15 102531392 11230512 0.10953242495722676 0.589445134817564 chr16 90354753 10056441 0.11129952399958418 0.6230859535587847 chr17 81195210 9461046 0.11652221849047499 0.6407373554051956 chr18 78077248 10296046 0.13186999111444092 1.1944076855910777 chr19 59128983 6822442 0.1153823667151522 1.1464227535997755 chr20 63025520 7770101 0.12328499629991153 0.6496323735796853 chr21 48129895 5138881 0.1067710827127298 0.63206876861794 chr22 51304566 4087745 0.07967604676745536 0.5695989874027226 chrMT 16571 62969 3.799951722889385 5.324663283687413 chrX 155270560 22509674 0.14497064994162448 0.7809445372835501 chrY 59373566 1175037 0.01979057481573534 0.32028037879718785