BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174029.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 = 1,277,410 number of mapped reads = 1,250,220 (97.87%) number of supplementary alignments = 124,166 (9.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 624,984 number of mapped paired reads (second in pair) = 625,236 number of mapped paired reads (both in pair) = 1,233,062 number of mapped paired reads (singletons) = 17,158 number of mapped bases = 147,299,035 bp number of sequenced bases = 147,250,850 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 970,538 duplication rate = 67.47% >>>>>>> Insert size mean insert size = 856,260.8884 std insert size = 9,059,716.4742 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 53.3065 >>>>>>> ACTG content number of A's = 44,551,312 bp (30.26%) number of C's = 28,941,459 bp (19.65%) number of T's = 44,185,644 bp (30.01%) number of G's = 29,570,638 bp (20.08%) number of N's = 1,797 bp (0%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,205,754 number of insertions = 12,125 mapped reads with insertion percentage = 0.94% number of deletions = 20,663 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.8747X There is a 0.95% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 12389725 0.049707900226254605 0.6577763359035247 chr2 243199373 12924741 0.053144631256923515 2.1681165190038607 chr3 198022430 11196991 0.05654405412558567 0.7063270982192791 chr4 191154276 8861867 0.04635976335679773 0.647982257220392 chr5 180915260 9088547 0.050236486408056454 0.6618767624711333 chr6 171115067 8099584 0.04733413685891261 0.6543478748250713 chr7 159138663 10382065 0.06523911162933423 0.7782513207520987 chr8 146364022 10552418 0.07209707587838765 0.9167346064738925 chr9 141213431 5706971 0.04041379746661633 0.5880327904441126 chr10 135534747 6496725 0.047934017982857194 0.6881576028340014 chr11 135006516 5889221 0.04362175378261002 0.6117447665124532 chr12 133851895 5925996 0.04427278373608383 0.6245536079282142 chr13 115169878 4250205 0.03690379006913596 0.5794590050767251 chr14 107349540 4507404 0.041988107261568146 0.6025335565998244 chr15 102531392 4095508 0.039943942241611234 0.5817995137231601 chr16 90354753 4018528 0.04447500398789204 0.6014419415811568 chr17 81195210 4149358 0.05110348258228534 0.6554312020980962 chr18 78077248 2695008 0.034517200196400366 0.5542030174383039 chr19 59128983 1908260 0.03227283648697289 0.5126481854724559 chr20 63025520 5473634 0.08684789907326429 0.8622870648993229 chr21 48129895 1696479 0.03524792647064782 0.5557691194908065 chr22 51304566 1237250 0.024115787277101224 0.44038735380180055 chrMT 16571 246243 14.859875686440166 22.347500467558614 chrX 155270560 5292726 0.034087118639876096 0.5451336489073427 chrY 59373566 213581 0.0035972405632499825 0.14984760784668957