BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084270.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,073,975 number of mapped reads = 887,865 (82.67%) number of supplementary alignments = 5,022 (0.47%) number of secondary alignments = 0 number of mapped bases = 57,439,625 bp number of sequenced bases = 57,420,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,590 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2317 >>>>>>> ACTG content number of A's = 16,640,223 bp (28.98%) number of C's = 10,616,291 bp (18.49%) number of T's = 17,510,989 bp (30.5%) number of G's = 12,652,236 bp (22.03%) number of N's = 682 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 489,276 number of insertions = 4,238 mapped reads with insertion percentage = 0.47% number of deletions = 12,224 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.1732X There is a 1.72% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4563640 0.01830944284788763 0.23315011506428163 chr2 243199373 4877047 0.02005369890488986 0.20471817200873693 chr3 198022430 3831745 0.019350055445739152 0.14686117277142346 chr4 191154276 3885922 0.02032872128897603 0.15237909564545243 chr5 180915260 3531535 0.019520382083855172 0.14757233873553394 chr6 171115067 3444554 0.020130045006498464 0.16269601100148354 chr7 159138663 3076954 0.019335049962057302 0.19398446903457572 chr8 146364022 3034212 0.020730586373200376 0.18768498856184473 chr9 141213431 2239114 0.015856239623552523 0.16178797270648188 chr10 135534747 2728527 0.020131568180077098 0.17890128689528856 chr11 135006516 2689912 0.019924312393929194 0.1606334121776961 chr12 133851895 2583939 0.019304463339872777 0.14718219992753445 chr13 115169878 1797762 0.015609654461907131 0.13195726937829702 chr14 107349540 1750355 0.016305193296589814 0.13964410102310434 chr15 102531392 1652039 0.016112518983454355 0.1356717147142893 chr16 90354753 1642888 0.018182640596671212 0.15160166945478892 chr17 81195210 1442508 0.017765924861823747 0.14992144927218087 chr18 78077248 1700171 0.021775498542161733 0.30439430154499447 chr19 59128983 1048482 0.017732116244921717 0.19708432696166875 chr20 63025520 1082652 0.017177993930077847 0.1398354475736177 chr21 48129895 762565 0.015843894943049427 0.13542161961226812 chr22 51304566 589220 0.011484747770792954 0.11268319387831278 chrMT 16571 4037 0.24361836944058898 0.49701982184929633 chrX 155270560 3345455 0.021545971110041723 0.16085489975768114 chrY 59373566 134390 0.0022634651925740826 0.05764749429454419