BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716234.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 = 1,206,944 number of mapped reads = 981,139 (81.29%) number of supplementary alignments = 3,794 (0.31%) number of secondary alignments = 0 number of mapped bases = 54,824,822 bp number of sequenced bases = 54,808,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,396 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6383 >>>>>>> ACTG content number of A's = 12,976,490 bp (23.68%) number of C's = 10,984,040 bp (20.04%) number of T's = 16,720,594 bp (30.51%) number of G's = 14,125,827 bp (25.77%) number of N's = 1,631 bp (0%) GC percentage = 45.81% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 289,872 number of insertions = 4,670 mapped reads with insertion percentage = 0.47% number of deletions = 9,250 mapped reads with deletion percentage = 0.93% homopolymer indels = 33.74% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.168X There is a 1.61% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% 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 5325375 0.0213655435586658 0.19600184119278374 chr2 243199373 4748492 0.019525099680252875 0.20315351772820445 chr3 198022430 3676951 0.018568356120061753 0.15240897948425258 chr4 191154276 3542192 0.018530540221867703 0.1696238293907874 chr5 180915260 3392934 0.018754272027688545 0.1476498727909355 chr6 171115067 2357213 0.013775601654061241 0.12935911716561987 chr7 159138663 3189304 0.020041038047429117 0.19266942731736328 chr8 146364022 3357880 0.02294197681995921 0.17558252867987365 chr9 141213431 2428258 0.017195658959663688 0.1501994778190358 chr10 135534747 2803286 0.020683153671286966 0.2525690152722008 chr11 135006516 2268927 0.01680605549438814 0.16474248652453857 chr12 133851895 2634085 0.019679101293261482 0.15194991596033017 chr13 115169878 982418 0.008530164458453277 0.10237806235940536 chr14 107349540 1737963 0.01618975731055764 0.139527250925555 chr15 102531392 1087765 0.010609092286584776 0.11298047512380818 chr16 90354753 1474625 0.016320392132553336 0.1473797000329198 chr17 81195210 2134003 0.026282375524368986 0.186354166408888 chr18 78077248 1498492 0.01919242850362759 0.18463551239096326 chr19 59128983 1483199 0.025084128370684137 0.2040031467424591 chr20 63025520 1385272 0.021979540985937126 0.1672925346246541 chr21 48129895 738076 0.015335084358692243 0.15433473309671242 chr22 51304566 588800 0.011476561364928027 0.11864091983005025 chrMT 16571 71753 4.330034397441313 3.8507107264829203 chrX 155270560 1734901 0.011173405956673306 0.12294252945536724 chrY 59373566 182658 0.003076419563547859 0.1079428575456447