BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708618.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,113,899 number of mapped reads = 2,243,636 (72.05%) number of supplementary alignments = 715 (0.02%) number of secondary alignments = 0 number of mapped bases = 109,149,042 bp number of sequenced bases = 109,128,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,751 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.258 >>>>>>> ACTG content number of A's = 32,111,348 bp (29.43%) number of C's = 20,511,606 bp (18.8%) number of T's = 34,498,720 bp (31.61%) number of G's = 21,997,322 bp (20.16%) number of N's = 9,523 bp (0.01%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 683,745 number of insertions = 4,991 mapped reads with insertion percentage = 0.22% number of deletions = 13,417 mapped reads with deletion percentage = 0.6% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.375X There is a 2.99% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 8538796 0.03425787252100768 0.6680785308513549 chr2 243199373 9403730 0.03866675264824799 0.3797051441364809 chr3 198022430 7531446 0.038033297541091686 0.22506242863570186 chr4 191154276 7385408 0.03863585034320655 0.22935024510397317 chr5 180915260 6887925 0.038072658989628624 0.22758299199871834 chr6 171115067 6516941 0.03808513834728534 0.2963896658615816 chr7 159138663 6253679 0.039297043736002735 0.543458233086339 chr8 146364022 5759418 0.03934995719098236 0.6927315973734984 chr9 141213431 4621361 0.03272607263539967 0.29447743304384744 chr10 135534747 5014814 0.03700020925261328 0.28994894213005296 chr11 135006516 4891098 0.03622860692146148 0.3201834797248601 chr12 133851895 5011595 0.03744134515241641 0.23063123630586368 chr13 115169878 3583507 0.031114967404932043 0.203849990868757 chr14 107349540 3309118 0.030825637445675128 0.21514787358914694 chr15 102531392 3054740 0.029793216891076637 0.19835090898654315 chr16 90354753 2840887 0.0314414782363469 0.21736256517273717 chr17 81195210 2574817 0.03171143962802732 0.24423830908076105 chr18 78077248 3060182 0.039194286151069256 0.5939317540650666 chr19 59128983 1911190 0.032322389174188906 0.5050510484203099 chr20 63025520 2097526 0.03328058221495039 0.2169085624685284 chr21 48129895 1419121 0.029485229502370616 0.21472853307512865 chr22 51304566 1108829 0.02161267673524419 0.16675578517664752 chrMT 16571 8958 0.5405829461106753 0.8755614238511472 chrX 155270560 6120431 0.039417845855647074 0.25520253901727785 chrY 59373566 243525 0.004101572743668454 0.08086656392671544