BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524605.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 = 1,333,580 number of mapped reads = 1,231,850 (92.37%) number of supplementary alignments = 2,454 (0.18%) number of secondary alignments = 0 number of mapped bases = 71,146,057 bp number of sequenced bases = 71,124,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,432 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2142 >>>>>>> ACTG content number of A's = 18,063,000 bp (25.4%) number of C's = 12,939,139 bp (18.19%) number of T's = 23,194,813 bp (32.61%) number of G's = 16,926,730 bp (23.8%) number of N's = 456 bp (0%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 337,103 number of insertions = 4,831 mapped reads with insertion percentage = 0.39% number of deletions = 12,982 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.2216X There is a 2.06% of reference with a coverageData >= 1X There is a 0.18% 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 6909103 0.027719501649707025 0.37276905653587367 chr2 243199373 6257209 0.025728721759492364 0.2678143762810964 chr3 198022430 4472926 0.022587976523669565 0.16625288796611112 chr4 191154276 3154962 0.01650479427412861 0.15674709392258815 chr5 180915260 4423002 0.024447921087474875 0.17191013549146864 chr6 171115067 4589964 0.026823844799125727 0.19187212712088078 chr7 159138663 4308510 0.0270739361433494 0.2814130753110661 chr8 146364022 6229576 0.04256220835472805 0.28990131460024593 chr9 141213431 2542455 0.018004342660578796 0.19265522548488878 chr10 135534747 3068503 0.02263997290672627 0.21770476557793578 chr11 135006516 4371756 0.03238181481551602 0.2300523061070967 chr12 133851895 2397860 0.017914277567755016 0.15009457135548074 chr13 115169878 1682952 0.014612779219927628 0.13412087165271422 chr14 107349540 1284128 0.011962119260129108 0.12352874251756707 chr15 102531392 1799655 0.01755223414893265 0.15394543347800618 chr16 90354753 2076103 0.022977241717433504 0.1724039109094594 chr17 81195210 1604289 0.019758419246652604 0.15610012443305918 chr18 78077248 1877524 0.024047005345270368 0.29745694801260464 chr19 59128983 1421174 0.024035150410078927 0.2605801653583703 chr20 63025520 1353325 0.021472651078483763 0.1645898455392326 chr21 48129895 611284 0.012700713350818654 0.13552983561586535 chr22 51304566 1351780 0.026348142190697022 0.17806544209315223 chrMT 16571 6751 0.407398467201738 0.7710066974385409 chrX 155270560 3179490 0.02047709494961569 0.1764395305404301 chrY 59373566 171776 0.002893139347567569 0.08831339213293285