BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008775.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,383,252 number of mapped reads = 1,236,769 (89.41%) number of supplementary alignments = 7,990 (0.58%) number of secondary alignments = 0 number of mapped bases = 82,536,080 bp number of sequenced bases = 82,494,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,899 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9143 >>>>>>> ACTG content number of A's = 22,150,463 bp (26.85%) number of C's = 15,836,788 bp (19.2%) number of T's = 25,562,366 bp (30.99%) number of G's = 18,809,599 bp (22.8%) number of N's = 135,764 bp (0.16%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 689,571 number of insertions = 5,973 mapped reads with insertion percentage = 0.48% number of deletions = 22,958 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.2634X There is a 2.18% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 7414483 0.029747099406424348 0.4268520328445408 chr2 243199373 5917989 0.024333899084517788 0.31450879946589755 chr3 198022430 9150982 0.04621184579948847 0.26431698383895724 chr4 191154276 3374691 0.017654279415648542 0.16897568759002404 chr5 180915260 3940181 0.02177915229483682 0.1726457387576658 chr6 171115067 4845402 0.028316629768201533 0.21749398055445585 chr7 159138663 4893212 0.03074810299241989 0.3035064729713557 chr8 146364022 7603946 0.051952289203968445 0.3297089188912281 chr9 141213431 2501224 0.01771236618420524 0.19119661328799833 chr10 135534747 4139125 0.030539216633502845 0.38002100247543874 chr11 135006516 3350340 0.024816135541191213 0.23454146976725154 chr12 133851895 2361663 0.017643851810988556 0.15690372435323985 chr13 115169878 1356476 0.011778044950260346 0.127317886482374 chr14 107349540 3398419 0.03165750873268763 0.21205332928830245 chr15 102531392 2867633 0.02796834163726169 0.19920580985344583 chr16 90354753 2286486 0.025305652708718047 0.2532804218553052 chr17 81195210 1792340 0.02207445488471549 0.19477323491670082 chr18 78077248 1218879 0.01561119316090649 0.2941931309831679 chr19 59128983 2116535 0.035795220763394496 0.3144157546987222 chr20 63025520 1858212 0.02948348541987436 0.20623565760819101 chr21 48129895 797156 0.016562595866872348 0.1637188443260242 chr22 51304566 961834 0.01874753213973197 0.15946308792633532 chrMT 16571 119022 7.182547824512703 4.820927353643895 chrX 155270560 4028229 0.02594328892740517 0.19721600930385408 chrY 59373566 241621 0.004069504600751115 0.15183190949339