BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548993.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,712,624 number of mapped reads = 7,545,429 (86.6%) number of secondary alignments = 0 number of mapped bases = 299,414,627 bp number of sequenced bases = 299,382,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 634,045 duplication rate = 7.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.032 >>>>>>> ACTG content number of A's = 89,902,225 bp (30.03%) number of C's = 59,275,692 bp (19.8%) number of T's = 90,243,281 bp (30.14%) number of G's = 59,958,521 bp (20.03%) number of N's = 2,917 bp (0%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 880,383 number of insertions = 9,306 mapped reads with insertion percentage = 0.12% number of deletions = 24,792 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0967X std coverageData = 0.7759X There is a 7.49% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24293826 0.09746746428366973 1.1954174063708876 chr2 243199373 26353825 0.10836304664321647 0.5823477208067699 chr3 198022430 21297174 0.10754930135944701 0.4019180782007754 chr4 191154276 21122819 0.11050142032920049 0.45527235072813044 chr5 180915260 19298391 0.10667088558477598 0.4069611416743951 chr6 171115067 18341396 0.10718749857369368 0.4771692117313455 chr7 159138663 16502012 0.10369580646784747 0.8041078595283379 chr8 146364022 15772130 0.10775961048679025 2.236590687891303 chr9 141213431 12773603 0.09045600627039506 0.524815752264246 chr10 135534747 14274113 0.1053170003703921 0.6410427641831838 chr11 135006516 13658474 0.10116899839115913 0.5187844018818378 chr12 133851895 13730082 0.10257667252301508 0.41269591761213675 chr13 115169878 10097333 0.08767338452854834 0.35856010131375776 chr14 107349540 9340122 0.08700663272520777 0.4477300138304768 chr15 102531392 8445106 0.0823660523403408 0.34666659544405587 chr16 90354753 7787535 0.08618843770177757 0.40694692237433105 chr17 81195210 7163453 0.08822506894187478 0.3987445103994141 chr18 78077248 8376931 0.10729029537516487 1.1167047782934743 chr19 59128983 4903292 0.08292535658866312 0.9478068928951233 chr20 63025520 6009540 0.09535089912784536 0.40741455864685644 chr21 48129895 3936669 0.08179259481035643 0.4411232745087104 chr22 51304566 2889669 0.056323817260241514 0.3236651227558039 chrMT 16571 11627 0.7016474563997345 1.221232978543062 chrX 155270560 10296817 0.06631532081806106 0.431126458780054 chrY 59373566 2738688 0.04612638560399084 0.484060247179973