BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524574.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 = 1,588,778 number of mapped reads = 1,431,662 (90.11%) number of supplementary alignments = 6,620 (0.42%) number of secondary alignments = 0 number of mapped bases = 82,115,341 bp number of sequenced bases = 82,089,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,528 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1988 >>>>>>> ACTG content number of A's = 19,346,725 bp (23.57%) number of C's = 14,643,708 bp (17.84%) number of T's = 26,916,755 bp (32.79%) number of G's = 21,181,276 bp (25.8%) number of N's = 1,227 bp (0%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 419,570 number of insertions = 5,280 mapped reads with insertion percentage = 0.37% number of deletions = 15,351 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2397X There is a 2.43% of reference with a coverageData >= 1X There is a 0.16% 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 6632638 0.026610316850524517 0.4101359370383889 chr2 243199373 6939887 0.028535793141210113 0.2743675570210786 chr3 198022430 5476109 0.027653983440158774 0.18020890131388181 chr4 191154276 5247578 0.027452056578634945 0.19410040166231565 chr5 180915260 4888666 0.027021855425573275 0.17695690875815603 chr6 171115067 4710548 0.027528540195703513 0.20642257100702666 chr7 159138663 4528564 0.028456717648809204 0.3156776469093008 chr8 146364022 4201376 0.02870497778477282 0.21586094219163238 chr9 141213431 3413973 0.024175979408077693 0.20940214075968938 chr10 135534747 3935943 0.029040102904386578 0.2477279716709835 chr11 135006516 3716588 0.02752895275069538 0.22080978428330753 chr12 133851895 3705264 0.02768181952149426 0.17961909184495178 chr13 115169878 2566479 0.022284290341959032 0.1606594441313898 chr14 107349540 2480390 0.023105734780046565 0.1667706642041665 chr15 102531392 2360988 0.02302697694770398 0.16969513312530887 chr16 90354753 2421404 0.02679885583882898 0.18914797441258463 chr17 81195210 2304923 0.02838742580997081 0.1914769174258168 chr18 78077248 2168014 0.0277675514382884 0.36594759053283243 chr19 59128983 1730870 0.029272784887911907 0.29778352477416026 chr20 63025520 1738919 0.02759071246060326 0.18181116314651055 chr21 48129895 1072930 0.022292381896947832 0.1694655866820629 chr22 51304566 978587 0.01907407227652993 0.14783323981204488 chrMT 16571 3060 0.1846599481021061 0.4896453956999046 chrX 155270560 4639746 0.029881685233826682 0.20907528569425832 chrY 59373566 251897 0.004242578254437337 0.11147677532161107