BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173910.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 = 3,350,814 number of mapped reads = 3,262,138 (97.35%) number of supplementary alignments = 325,970 (9.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,634,541 number of mapped paired reads (second in pair) = 1,627,597 number of mapped paired reads (both in pair) = 3,203,548 number of mapped paired reads (singletons) = 58,590 number of mapped bases = 385,874,219 bp number of sequenced bases = 385,654,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,510,555 duplication rate = 64.06% >>>>>>> Insert size mean insert size = 960,930.8739 std insert size = 9,224,335.4178 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.6855 >>>>>>> ACTG content number of A's = 116,230,749 bp (30.14%) number of C's = 75,472,192 bp (19.57%) number of T's = 115,890,391 bp (30.05%) number of G's = 78,056,622 bp (20.24%) number of N's = 4,633 bp (0%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 4,026,730 number of insertions = 40,957 mapped reads with insertion percentage = 1.21% number of deletions = 88,633 mapped reads with deletion percentage = 2.65% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.1246X std coverageData = 1.9126X There is a 2.69% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 1.61% of reference with a coverageData >= 3X There is a 1.31% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% 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 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% 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 34499463 0.1384127464220039 1.7367962504223493 chr2 243199373 41156659 0.1692301196845602 5.2699588105871 chr3 198022430 28178067 0.14229734985072146 1.0774308654752447 chr4 191154276 22016618 0.11517721947271532 1.1217309316995256 chr5 180915260 25847495 0.14287072853887506 1.0777567147120868 chr6 171115067 22760496 0.13301281061357384 1.0795150703729683 chr7 159138663 25486744 0.16015431774741 1.7783207411871915 chr8 146364022 16823626 0.11494372571969906 1.0991945696011673 chr9 141213431 15196045 0.10761047934597666 1.116647979582254 chr10 135534747 15579372 0.1149474385339724 1.8977462227242266 chr11 135006516 17572800 0.13016260637375457 1.0500014598817387 chr12 133851895 14359167 0.10727653127361401 0.9409918753412916 chr13 115169878 12036573 0.1045114678336292 0.9308451245558609 chr14 107349540 9729323 0.09063218156314409 0.8571854592879288 chr15 102531392 12680243 0.12367181165354704 0.9952753361852101 chr16 90354753 15463957 0.17114713378719545 1.511996687894158 chr17 81195210 9275450 0.11423641862617265 1.0810233874219914 chr18 78077248 6313206 0.08085845956045992 1.3945822417568505 chr19 59128983 7853661 0.13282252799781794 1.7085140219872046 chr20 63025520 11202086 0.1777388905319623 1.1974037287220893 chr21 48129895 5584641 0.1160326861298991 0.9947004489363646 chr22 51304566 1797833 0.03504235860800382 0.4995343154416257 chrMT 16571 1268399 76.54329853358277 59.827101711768314 chrX 155270560 12670263 0.08160119342649373 0.8095782042222534 chrY 59373566 522032 0.008792330243394847 0.37970246712931743