BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716911.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 = 1,392,420 number of mapped reads = 954,729 (68.57%) number of supplementary alignments = 3,749 (0.27%) number of secondary alignments = 0 number of mapped bases = 53,249,051 bp number of sequenced bases = 53,234,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,618 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2587 >>>>>>> ACTG content number of A's = 12,842,843 bp (24.13%) number of C's = 11,052,933 bp (20.76%) number of T's = 15,783,472 bp (29.65%) number of G's = 13,553,531 bp (25.46%) number of N's = 1,473 bp (0%) GC percentage = 46.22% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 283,406 number of insertions = 4,109 mapped reads with insertion percentage = 0.43% number of deletions = 8,589 mapped reads with deletion percentage = 0.89% homopolymer indels = 33.31% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.167X There is a 1.57% 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 5590390 0.022428790658860585 0.19927937919422628 chr2 243199373 4589604 0.018871775627480752 0.2012812957827061 chr3 198022430 3497704 0.01766317078322895 0.14769176098185216 chr4 191154276 3731866 0.019522796340689756 0.17221536415591035 chr5 180915260 3250723 0.01796820787809718 0.14484553681059764 chr6 171115067 2204116 0.012880899611253988 0.12536950442192754 chr7 159138663 2997193 0.018833845550153955 0.18141222519010627 chr8 146364022 2930284 0.0200205211633225 0.16066113247312255 chr9 141213431 2407418 0.01704808092935579 0.15514470329231547 chr10 135534747 2754218 0.02032112104802173 0.27423252216224026 chr11 135006516 2145375 0.01589089966590946 0.16228865723249888 chr12 133851895 2578784 0.019265950624008724 0.15125174031140887 chr13 115169878 873692 0.007586115529270596 0.09548105084079261 chr14 107349540 1641301 0.015289315631906759 0.13797174785272995 chr15 102531392 1049595 0.010236816057271513 0.11117084838560229 chr16 90354753 1589914 0.01759635157211929 0.15653088763245254 chr17 81195210 2166549 0.026683211977652378 0.18552351431140743 chr18 78077248 1399149 0.017920060399669823 0.18615268887417152 chr19 59128983 1299048 0.0219697335230677 0.19357356913423257 chr20 63025520 1462936 0.023211803726490475 0.1724677475372961 chr21 48129895 685132 0.014235061181828882 0.15168199919350964 chr22 51304566 564977 0.011012216729403774 0.1155305611863292 chrMT 16571 21643 1.3060768812986543 1.5070172496849292 chrX 155270560 1643383 0.010583996090437234 0.11771771652997422 chrY 59373566 174057 0.002931557117522636 0.10537793794713127