BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174060.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 = 2,353,814 number of mapped reads = 2,291,453 (97.35%) number of supplementary alignments = 235,495 (10%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,145,632 number of mapped paired reads (second in pair) = 1,145,821 number of mapped paired reads (both in pair) = 2,248,998 number of mapped paired reads (singletons) = 42,455 number of mapped bases = 271,533,222 bp number of sequenced bases = 271,382,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,815,818 duplication rate = 64.61% >>>>>>> Insert size mean insert size = 1,212,179.1368 std insert size = 10,398,609.8166 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.6975 >>>>>>> ACTG content number of A's = 81,495,730 bp (30.03%) number of C's = 53,340,875 bp (19.66%) number of T's = 81,244,502 bp (29.94%) number of G's = 55,298,265 bp (20.38%) number of N's = 3,021 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,793,517 number of insertions = 28,760 mapped reads with insertion percentage = 1.22% number of deletions = 61,329 mapped reads with deletion percentage = 2.61% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0877X std coverageData = 1.4794X There is a 1.78% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 23417920 0.09395330653960537 1.2580620375387825 chr2 243199373 27601645 0.11349389868698387 3.95411724340963 chr3 198022430 20544345 0.10374756536418626 0.9524537977932127 chr4 191154276 16002745 0.08371638518826542 0.9664278226826276 chr5 180915260 18350070 0.10142908895579068 0.9468873210036306 chr6 171115067 15451350 0.09029800981815353 0.9072991402248622 chr7 159138663 19624674 0.12331807764402293 1.384857223717757 chr8 146364022 11294818 0.07716936065066592 0.9050232611609254 chr9 141213431 10978021 0.07774062935982343 0.8877263647245214 chr10 135534747 10472633 0.07726898992182425 1.2718189068495116 chr11 135006516 13150672 0.09740768364098812 0.9376139456070374 chr12 133851895 9445998 0.07057052124663607 0.7816000490605421 chr13 115169878 8645615 0.07506836987358795 0.8096755871658992 chr14 107349540 7166895 0.06676223298208823 0.7664707497583878 chr15 102531392 9148829 0.08922954054890818 0.869538613340338 chr16 90354753 10809648 0.11963563222844514 1.1476025028487176 chr17 81195210 6410137 0.07894723100044941 0.9073362646314217 chr18 78077248 4376247 0.05605022092991802 1.1888816058202114 chr19 59128983 5032957 0.08511827440022095 1.2618926754610367 chr20 63025520 6782369 0.10761305896405139 0.9785263662263378 chr21 48129895 4125660 0.08571928112454848 0.8836378556807403 chr22 51304566 2384108 0.0464697040805296 0.5922082623817558 chrMT 16571 1286618 77.64274938144952 59.09287145853581 chrX 155270560 8667865 0.0558242657204302 0.6897053247793677 chrY 59373566 361383 0.00608659752725649 0.3216980257106775