BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,909,123 number of mapped reads = 1,676,148 (87.8%) number of supplementary alignments = 15,325 (0.8%) number of secondary alignments = 0 number of mapped bases = 113,338,552 bp number of sequenced bases = 113,284,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,064 duplication rate = 5.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5032 >>>>>>> ACTG content number of A's = 31,926,846 bp (28.18%) number of C's = 21,035,853 bp (18.57%) number of T's = 35,864,833 bp (31.66%) number of G's = 24,456,275 bp (21.59%) number of N's = 1,143 bp (0%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 849,772 number of insertions = 9,631 mapped reads with insertion percentage = 0.57% number of deletions = 30,776 mapped reads with deletion percentage = 1.81% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.4635X There is a 2.48% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10342389 0.04149393473326592 0.533141167098679 chr2 243199373 8682105 0.03569953693918446 0.39554073408921525 chr3 198022430 10692517 0.05399649423552675 0.31897826427806614 chr4 191154276 5345242 0.02796297373959869 0.277470801963941 chr5 180915260 7285282 0.04026902982092279 0.2762844316162482 chr6 171115067 10995739 0.06425932673713648 0.4104295447247346 chr7 159138663 5875352 0.03691970190801465 0.39230653374393554 chr8 146364022 7673662 0.0524286084458652 1.4600655335026063 chr9 141213431 4614278 0.03267591451694138 0.32949014375115826 chr10 135534747 3668741 0.027068637978126746 0.34473222847079976 chr11 135006516 5341788 0.03956689023809784 0.3536225897471504 chr12 133851895 4167481 0.031135016803460272 0.24548118960195953 chr13 115169878 3414803 0.029650139943709936 0.23745353087884835 chr14 107349540 4295509 0.040014228286399736 0.28476145745344494 chr15 102531392 2057715 0.02006912185489494 0.19206009414555908 chr16 90354753 2867673 0.031737931927056456 0.25699937883382357 chr17 81195210 2818798 0.03471630900394247 0.2894288087741235 chr18 78077248 2069661 0.02650786308451855 0.5486062778443438 chr19 59128983 1969817 0.03331389954736749 0.3579271873393709 chr20 63025520 1837189 0.02914992212678293 0.2410283937330482 chr21 48129895 1339532 0.027831600297486624 0.25930249562913277 chr22 51304566 1404111 0.02736814887002455 0.2204634260468919 chrMT 16571 148565 8.965361173133788 9.394378184627282 chrX 155270560 4124018 0.02656020561785827 0.236149952971528 chrY 59373566 306585 0.00516366155268491 0.16368521995567728