BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173997.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 = 7,075,872 number of mapped reads = 6,932,709 (97.98%) number of supplementary alignments = 877,837 (12.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,466,550 number of mapped paired reads (second in pair) = 3,466,159 number of mapped paired reads (both in pair) = 6,840,190 number of mapped paired reads (singletons) = 92,519 number of mapped bases = 788,141,273 bp number of sequenced bases = 787,625,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,602,165 duplication rate = 65.56% >>>>>>> Insert size mean insert size = 1,069,017.3114 std insert size = 9,515,054.6628 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.6539 >>>>>>> ACTG content number of A's = 235,661,360 bp (29.92%) number of C's = 156,331,527 bp (19.85%) number of T's = 233,612,444 bp (29.66%) number of G's = 162,014,239 bp (20.57%) number of N's = 5,844 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 6,566,402 number of insertions = 86,403 mapped reads with insertion percentage = 1.2% number of deletions = 219,884 mapped reads with deletion percentage = 3.1% homopolymer indels = 41.71% >>>>>>> Coverage mean coverageData = 0.2546X std coverageData = 4.2069X There is a 5.24% of reference with a coverageData >= 1X There is a 3.98% of reference with a coverageData >= 2X There is a 3.01% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 1.86% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 1.18% of reference with a coverageData >= 7X There is a 1.02% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.52% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 61559379 0.24697783601510065 2.1776120526266 chr2 243199373 73513446 0.30227646187229273 13.460016243386015 chr3 198022430 53683550 0.2710983296185185 1.6009720019622466 chr4 191154276 54258833 0.2838483874668856 2.3139047066389016 chr5 180915260 46718840 0.25823603824243463 1.5469044562167824 chr6 171115067 48501644 0.28344461332560505 1.8837191488783822 chr7 159138663 43345453 0.2723753749269591 2.21243153361325 chr8 146364022 39889939 0.2725392378189771 2.4946790222827238 chr9 141213431 34163799 0.24193023820800727 2.0306291458578642 chr10 135534747 38714534 0.2856428691308215 2.6544577165540195 chr11 135006516 35803581 0.2651989108436811 1.631694517182616 chr12 133851895 35409809 0.2645446969577831 1.625036652891637 chr13 115169878 25558767 0.22192232416882476 1.448581106664884 chr14 107349540 24383552 0.22714165333172365 1.472924940545814 chr15 102531392 22531190 0.21974918666860585 1.4579340226590727 chr16 90354753 24226317 0.2681244339188222 1.9728376538723507 chr17 81195210 21782219 0.2682697538438536 1.7333447930676111 chr18 78077248 23683075 0.303328762304737 2.7796580813450467 chr19 59128983 15124981 0.2557964002188233 1.8280266996686745 chr20 63025520 16899336 0.2681348126917477 1.6756752279576108 chr21 48129895 10638994 0.2210475215040465 1.8584581316358293 chr22 51304566 9783767 0.19069973226164705 1.573987650858933 chrMT 16571 1029047 62.09926980870195 57.49467958669209 chrX 155270560 21390662 0.13776379759305304 1.1453235859988002 chrY 59373566 5546559 0.09341798671819712 1.574939664025553