BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524614.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 = 1,769,165 number of mapped reads = 1,660,490 (93.86%) number of supplementary alignments = 3,575 (0.2%) number of secondary alignments = 0 number of mapped bases = 97,323,788 bp number of sequenced bases = 97,292,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,441 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4285 >>>>>>> ACTG content number of A's = 23,171,203 bp (23.82%) number of C's = 19,052,343 bp (19.58%) number of T's = 30,229,468 bp (31.07%) number of G's = 24,838,902 bp (25.53%) number of N's = 602 bp (0%) GC percentage = 45.11% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 434,975 number of insertions = 5,049 mapped reads with insertion percentage = 0.3% number of deletions = 18,151 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.2589X There is a 2.77% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 10360361 0.04156603886655913 0.43136602486908143 chr2 243199373 8494533 0.034928268503389606 0.30124703028707017 chr3 198022430 5873614 0.02966135704929992 0.1915362542603897 chr4 191154276 4049534 0.021184637271729145 0.18396848776740127 chr5 180915260 5864090 0.03241346252383574 0.20005390549019583 chr6 171115067 6670830 0.03898446885451647 0.2343976366839155 chr7 159138663 5677308 0.03567522745871002 0.33354236174806273 chr8 146364022 8253981 0.056393510421570675 0.3335648620379932 chr9 141213431 3534259 0.025027782236946003 0.2333997779346666 chr10 135534747 4051879 0.029895499786486486 0.25479324468447795 chr11 135006516 4935194 0.03655522819357845 0.25450478364927104 chr12 133851895 3273006 0.024452444248174447 0.17566619393356922 chr13 115169878 2526283 0.021935275471942413 0.16565547987630913 chr14 107349540 1748179 0.016284923065343362 0.14522653777189792 chr15 102531392 2628694 0.025637943157935474 0.18417209895328196 chr16 90354753 3086253 0.034157063104361535 0.21449012930676148 chr17 81195210 2660081 0.03276155083532637 0.20535872436669853 chr18 78077248 2287033 0.029291926375273884 0.34660596217906986 chr19 59128983 2140352 0.03619801815295893 0.31851355427540134 chr20 63025520 1973456 0.0313120145617204 0.19912614143409701 chr21 48129895 874315 0.018165736700651434 0.16310980572357495 chr22 51304566 2238620 0.04363393308891844 0.23402710544721528 chrMT 16571 10129 0.6112485667732787 0.967321443927909 chrX 155270560 3909389 0.025177915246779557 0.19529980083002124 chrY 59373566 202415 0.0034091770738513497 0.10053005501686887