BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174016.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 = 4,568,176 number of mapped reads = 4,449,788 (97.41%) number of supplementary alignments = 465,901 (10.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,226,757 number of mapped paired reads (second in pair) = 2,223,031 number of mapped paired reads (both in pair) = 4,367,340 number of mapped paired reads (singletons) = 82,448 number of mapped bases = 526,598,744 bp number of sequenced bases = 526,308,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,483,927 duplication rate = 65.12% >>>>>>> Insert size mean insert size = 877,065.3602 std insert size = 8,444,523.4923 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.6762 >>>>>>> ACTG content number of A's = 157,964,709 bp (30.01%) number of C's = 103,321,592 bp (19.63%) number of T's = 157,887,216 bp (30%) number of G's = 107,128,206 bp (20.35%) number of N's = 6,367 bp (0%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 5,304,703 number of insertions = 56,493 mapped reads with insertion percentage = 1.22% number of deletions = 119,585 mapped reads with deletion percentage = 2.62% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.1701X std coverageData = 2.4747X There is a 3.53% of reference with a coverageData >= 1X There is a 2.8% of reference with a coverageData >= 2X There is a 2.17% of reference with a coverageData >= 3X There is a 1.78% of reference with a coverageData >= 4X There is a 1.36% of reference with a coverageData >= 5X There is a 1.1% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% 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% 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 38546194 0.1546483368641236 1.8206731873515583 chr2 243199373 47150477 0.1938758164479314 7.210292041865698 chr3 198022430 41146483 0.20778698150507496 1.333527892873108 chr4 191154276 26701427 0.13968521949255272 1.332182023017124 chr5 180915260 32919516 0.18196096890886926 1.2253616042662603 chr6 171115067 29900976 0.17474192380732903 1.4082076804777746 chr7 159138663 30012701 0.1885946534564011 1.7110261063165448 chr8 146364022 31087260 0.2123968689518521 1.6408950680456718 chr9 141213431 21954516 0.15547045238211088 1.4603849201500254 chr10 135534747 23128761 0.1706482028553165 2.32020687802387 chr11 135006516 18464577 0.13676804310689716 1.1138358700309199 chr12 133851895 23884171 0.17843730191492618 1.224939906909101 chr13 115169878 12603878 0.1094372783828077 0.9602549316492507 chr14 107349540 16069640 0.14969453991139597 1.1197371850313762 chr15 102531392 18478495 0.18022280434854526 1.2118142740843216 chr16 90354753 18439592 0.2040799336809653 1.6608781049227528 chr17 81195210 22082480 0.27196776755673147 1.6370938991295054 chr18 78077248 10100373 0.12936384489371347 2.130566059984875 chr19 59128983 8588910 0.14525719138446877 1.4796918866874724 chr20 63025520 24230432 0.38445429724340235 1.9586958328143529 chr21 48129895 6796440 0.14121036416140115 1.1499376476176875 chr22 51304566 4450910 0.08675465649587602 0.8203586593726685 chrMT 16571 731993 44.17313378794279 35.706104839521984 chrX 155270560 18150724 0.11689739510181453 0.979118401177876 chrY 59373566 977818 0.01646891143442521 0.7658803274949214