BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238626.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,012,124 number of mapped reads = 2,345,171 (77.86%) number of supplementary alignments = 17,772 (0.59%) number of secondary alignments = 0 number of mapped bases = 140,006,939 bp number of sequenced bases = 139,952,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,100,179 duplication rate = 24.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7223 >>>>>>> ACTG content number of A's = 34,014,213 bp (24.3%) number of C's = 23,741,036 bp (16.96%) number of T's = 48,349,769 bp (34.55%) number of G's = 33,844,178 bp (24.18%) number of N's = 2,988 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 790,368 number of insertions = 9,951 mapped reads with insertion percentage = 0.42% number of deletions = 32,597 mapped reads with deletion percentage = 1.38% homopolymer indels = 41.65% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.9091X There is a 1.09% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 9365488 0.03757458241197321 0.7390949926644219 chr2 243199373 12611098 0.05185497743861371 1.8030865621347465 chr3 198022430 9006521 0.0454823274312915 0.6860846067820447 chr4 191154276 10068759 0.05267346988356149 0.7390430039385392 chr5 180915260 8801842 0.04865173894120375 0.7015300215065691 chr6 171115067 6785813 0.03965643189094506 0.8474566049443298 chr7 159138663 7605869 0.04779397323452441 0.8382485955103561 chr8 146364022 6987767 0.047742381662619245 0.7894647599116457 chr9 141213431 6089588 0.04312329186308064 0.6970472866041362 chr10 135534747 7436045 0.05486449168640127 0.8205904854945691 chr11 135006516 6190384 0.04585248314977627 0.6928814220308982 chr12 133851895 6632898 0.049554008929048037 0.7207733235559368 chr13 115169878 5181692 0.044991729521498665 0.8141376109119667 chr14 107349540 3495331 0.032560279252244584 0.5975151486322227 chr15 102531392 3978060 0.03879845891490481 0.7092526589278042 chr16 90354753 3656971 0.04047347680757868 0.6512322507774275 chr17 81195210 3633309 0.04474782440983895 0.656218883520216 chr18 78077248 3879554 0.049688662182355604 1.8709085142097401 chr19 59128983 2786931 0.047133078544577704 0.7942510186704179 chr20 63025520 2536308 0.04024255571393937 0.6491471694333882 chr21 48129895 2239726 0.04653502776185155 0.7135806659328808 chr22 51304566 1663352 0.03242112992438139 0.5548942347436739 chrMT 16571 224105 13.523927342948525 15.247011572126059 chrX 155270560 8661477 0.05578312463096675 0.7770601829665434 chrY 59373566 488051 0.00822000484188536 0.33853801402281436