BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173867.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 = 4,813,198 number of mapped reads = 4,671,385 (97.05%) number of supplementary alignments = 462,357 (9.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,343,904 number of mapped paired reads (second in pair) = 2,327,481 number of mapped paired reads (both in pair) = 4,575,102 number of mapped paired reads (singletons) = 96,283 number of mapped bases = 548,144,649 bp number of sequenced bases = 547,836,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,529,278 duplication rate = 63.58% >>>>>>> Insert size mean insert size = 857,372.2069 std insert size = 8,429,012.3101 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.663 >>>>>>> ACTG content number of A's = 165,575,801 bp (30.22%) number of C's = 106,601,705 bp (19.46%) number of T's = 165,093,634 bp (30.14%) number of G's = 110,559,111 bp (20.18%) number of N's = 6,654 bp (0%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 5,614,065 number of insertions = 57,976 mapped reads with insertion percentage = 1.2% number of deletions = 121,519 mapped reads with deletion percentage = 2.54% homopolymer indels = 42.95% >>>>>>> Coverage mean coverageData = 0.1771X std coverageData = 2.6891X There is a 3.93% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 2.28% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.36% of reference with a coverageData >= 5X There is a 1.09% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% 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 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.02% 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 50046241 0.200786825722693 1.6174526270054141 chr2 243199373 41602909 0.17106503395467224 7.831826986626658 chr3 198022430 33876000 0.17107152962419458 1.1695294698011536 chr4 191154276 34414556 0.1800355017954189 1.5202299218659756 chr5 180915260 28164230 0.15567636472456772 1.0958498985403302 chr6 171115067 27129639 0.15854617290948436 1.1574840816694456 chr7 159138663 43613874 0.2740620863454156 2.680733404581817 chr8 146364022 54271298 0.37079671123003166 2.077029224834467 chr9 141213431 18722656 0.1325841024286139 1.3366548742463686 chr10 135534747 25840630 0.19065686528340958 3.4044228371816097 chr11 135006516 23312110 0.17267396189973527 1.1827910529670256 chr12 133851895 21400816 0.15988429599745302 1.1157206292562154 chr13 115169878 14374315 0.12480967462690201 0.9943097497655572 chr14 107349540 18621335 0.17346450669467237 1.1785107281109384 chr15 102531392 13586396 0.13250962202873437 1.0017435215474237 chr16 90354753 13156433 0.1456086432995949 1.4730120790177688 chr17 81195210 13821812 0.17022940146346072 1.3109870434417414 chr18 78077248 9732217 0.12464856599453915 1.6555492421129876 chr19 59128983 7138495 0.12072751192084599 1.1841832312032583 chr20 63025520 19187558 0.30444108989501395 1.5746180062952997 chr21 48129895 6784870 0.14096997302819797 1.1398890594050646 chr22 51304566 5666719 0.11045252775357266 0.8919609879847163 chrMT 16571 1563564 94.35544022690242 68.32705369231682 chrX 155270560 20941476 0.13487087313911922 1.0209983991441038 chrY 59373566 1174500 0.019781530386771783 0.8981476203791023