BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716957.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 = 1,556,047 number of mapped reads = 1,419,366 (91.22%) number of supplementary alignments = 9,160 (0.59%) number of secondary alignments = 0 number of mapped bases = 83,233,088 bp number of sequenced bases = 83,209,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,858 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0181 >>>>>>> ACTG content number of A's = 20,705,579 bp (24.88%) number of C's = 15,505,653 bp (18.63%) number of T's = 25,336,151 bp (30.45%) number of G's = 21,660,696 bp (26.03%) number of N's = 1,068 bp (0%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 415,217 number of insertions = 4,889 mapped reads with insertion percentage = 0.34% number of deletions = 14,940 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2387X There is a 2.41% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6655092 0.026700402884853796 0.3788394358118931 chr2 243199373 6991326 0.02874730273256091 0.30694330820798615 chr3 198022430 5482218 0.02768483348073246 0.1816600353909883 chr4 191154276 5313034 0.02779448156315373 0.20322004912657546 chr5 180915260 5022337 0.02776071515470834 0.18203351330296053 chr6 171115067 4803848 0.0280737873304868 0.1984440097349734 chr7 159138663 4530643 0.028469781727398325 0.2996125224850339 chr8 146364022 4197158 0.02867615922716308 0.24300864826477855 chr9 141213431 3520500 0.024930348162137638 0.20262283537104153 chr10 135534747 4006298 0.02955919488306567 0.25007247619171213 chr11 135006516 3744277 0.027734046555204787 0.21691068858760704 chr12 133851895 3733005 0.027889070976544635 0.18473979084890021 chr13 115169878 2620361 0.022752138367290793 0.16477535479306638 chr14 107349540 2609767 0.024310928579666016 0.1753956374164293 chr15 102531392 2475134 0.02414025550340719 0.17273179768746713 chr16 90354753 2447205 0.02708440805543456 0.18830880888740906 chr17 81195210 2347606 0.028913109529490718 0.20138694296432855 chr18 78077248 2170606 0.02780074932968949 0.33532641421380177 chr19 59128983 1793629 0.030334176388591025 0.30594528322061676 chr20 63025520 1820777 0.028889519673935257 0.18811238680885084 chr21 48129895 1080604 0.022451825419523563 0.17878446141414084 chr22 51304566 1041570 0.020301701801746067 0.15597165421578096 chrMT 16571 17958 1.0837004405286343 1.2872434301304345 chrX 155270560 4554934 0.02933546449500794 0.19943370698124938 chrY 59373566 253201 0.004264540890132824 0.12190588651145198