BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082948.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 = 1,832,380 number of mapped reads = 1,694,234 (92.46%) number of supplementary alignments = 17,165 (0.94%) number of secondary alignments = 0 number of mapped bases = 114,569,238 bp number of sequenced bases = 114,525,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,807 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3941 >>>>>>> ACTG content number of A's = 32,097,321 bp (28.03%) number of C's = 20,826,312 bp (18.18%) number of T's = 36,817,394 bp (32.15%) number of G's = 24,778,764 bp (21.64%) number of N's = 5,655 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 810,231 number of insertions = 9,581 mapped reads with insertion percentage = 0.56% number of deletions = 26,671 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.2965X There is a 3.13% of reference with a coverageData >= 1X There is a 0.43% 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 9901281 0.039724197918848916 0.42547722097586177 chr2 243199373 11701548 0.04811504180975006 0.3985110651631681 chr3 198022430 8949531 0.04519453175077187 0.2425841943989596 chr4 191154276 7610681 0.03981433823640963 0.2300765531841421 chr5 180915260 5887380 0.03254219682739864 0.20639804224973524 chr6 171115067 8007572 0.04679641682283887 0.2910418795235767 chr7 159138663 6687523 0.04202324484779667 0.44265910565576916 chr8 146364022 9204403 0.06288705977210711 0.3987846319331668 chr9 141213431 3484915 0.024678353718351337 0.2454274077895889 chr10 135534747 4441232 0.03276821699456893 0.23313453675656048 chr11 135006516 4707366 0.03486769483037396 0.2731066829516151 chr12 133851895 3764327 0.02812307588174228 0.19314084504757764 chr13 115169878 2759758 0.023962498249759368 0.17687168365374026 chr14 107349540 2153465 0.020060309527176363 0.17726808827244434 chr15 102531392 1899128 0.01852240531368188 0.161493543725346 chr16 90354753 4496047 0.04975993902611853 0.2635763056115147 chr17 81195210 2801552 0.03450390731177369 0.24059195917506368 chr18 78077248 3239178 0.041486836216358444 0.45676983180622543 chr19 59128983 1601051 0.027077262600643748 0.30851152106822416 chr20 63025520 2223212 0.03527479027543128 0.22156362922154665 chr21 48129895 2247836 0.04670353010327573 0.25040056971679436 chr22 51304566 1450698 0.028276196703427917 0.19062539356729846 chrMT 16571 63335 3.8220385009957156 3.133887234443083 chrX 155270560 5096218 0.032821534230313844 0.21964817389554026 chrY 59373566 190001 0.003200094129431269 0.06772657306887646