BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173974.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 13,424,230 number of mapped reads = 13,044,658 (97.17%) number of supplementary alignments = 1,289,610 (9.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,540,772 number of mapped paired reads (second in pair) = 6,503,886 number of mapped paired reads (both in pair) = 12,796,834 number of mapped paired reads (singletons) = 247,824 number of mapped bases = 1,542,226,547 bp number of sequenced bases = 1,541,367,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,279,525 duplication rate = 65.11% >>>>>>> Insert size mean insert size = 907,435.5983 std insert size = 8,712,155.9945 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.7469 >>>>>>> ACTG content number of A's = 458,763,328 bp (29.76%) number of C's = 307,155,362 bp (19.93%) number of T's = 457,597,497 bp (29.69%) number of G's = 317,833,197 bp (20.62%) number of N's = 18,512 bp (0%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 16,193,550 number of insertions = 160,775 mapped reads with insertion percentage = 1.19% number of deletions = 346,265 mapped reads with deletion percentage = 2.59% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.4982X std coverageData = 6.7127X There is a 9.42% of reference with a coverageData >= 1X There is a 7.6% of reference with a coverageData >= 2X There is a 6.05% of reference with a coverageData >= 3X There is a 5.06% of reference with a coverageData >= 4X There is a 3.98% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 2.52% of reference with a coverageData >= 7X There is a 2.07% of reference with a coverageData >= 8X There is a 1.58% of reference with a coverageData >= 9X There is a 1.32% of reference with a coverageData >= 10X There is a 1.02% of reference with a coverageData >= 11X There is a 0.87% of reference with a coverageData >= 12X There is a 0.67% of reference with a coverageData >= 13X There is a 0.58% of reference with a coverageData >= 14X There is a 0.45% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149922035 0.6014911192538213 3.3421312752067007 chr2 243199373 114360863 0.4702350240023028 21.083525578615976 chr3 198022430 94431803 0.4768742763130419 2.066182068899358 chr4 191154276 89004841 0.4656178394879328 2.8670151512028643 chr5 180915260 75321202 0.4163341555599014 1.9000193241883832 chr6 171115067 75506190 0.44125974014900743 2.1486448462044283 chr7 159138663 134071913 0.8424848523454039 6.2179710098628265 chr8 146364022 135567647 0.9262361415567003 4.245270872231302 chr9 141213431 56229938 0.3981911465631056 2.854930657966696 chr10 135534747 68635207 0.5064030333121882 6.822574495459541 chr11 135006516 66290577 0.4910176113277377 2.16660270254489 chr12 133851895 60180140 0.44960245052937053 2.0200503344643983 chr13 115169878 36423421 0.31625822335246373 1.6618729776587395 chr14 107349540 53798432 0.5011519564965067 2.129960902494911 chr15 102531392 39062500 0.38098088047024664 1.8463708728028112 chr16 90354753 38738019 0.4287324984442158 2.9337559907375943 chr17 81195210 41644185 0.5128896766200863 2.5844710149418098 chr18 78077248 24662998 0.3158794480051346 3.6138615404532035 chr19 59128983 22851517 0.38646896734212394 2.6266449054652545 chr20 63025520 65645152 1.0415646233462255 3.186092611843345 chr21 48129895 18977997 0.39430788286573243 2.1818158510611174 chr22 51304566 20772119 0.4048785638299718 1.821731210900886 chrMT 16571 4375781 264.06257920463463 170.32232091123126 chrX 155270560 53195021 0.34259566655778145 1.7630741042848777 chrY 59373566 2557049 0.04306712856020809 1.639872918702252