BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082961.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 = 3,506,845 number of mapped reads = 2,700,768 (77.01%) number of supplementary alignments = 16,045 (0.46%) number of secondary alignments = 0 number of mapped bases = 183,457,127 bp number of sequenced bases = 183,379,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,508 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1793 >>>>>>> ACTG content number of A's = 51,788,297 bp (28.24%) number of C's = 33,840,237 bp (18.45%) number of T's = 58,401,917 bp (31.85%) number of G's = 39,330,550 bp (21.45%) number of N's = 18,027 bp (0.01%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,767,027 number of insertions = 17,459 mapped reads with insertion percentage = 0.64% number of deletions = 44,696 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0593X std coverageData = 0.5695X There is a 4.85% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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% 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 13528189 0.05427544752235542 1.1242779058589512 chr2 243199373 13768291 0.05661318460718236 0.6737233420817511 chr3 198022430 12849755 0.06489040155703574 0.2999280223076626 chr4 191154276 12989560 0.06795327978956642 0.3351343461489555 chr5 180915260 12499826 0.0690921595005308 0.3147246558242907 chr6 171115067 10294210 0.06015957671337031 0.33031071200337697 chr7 159138663 10398111 0.06533994193478929 0.556811134783989 chr8 146364022 8684322 0.05933372068717817 0.6710195071015362 chr9 141213431 8713099 0.06170163091639633 0.649806435514174 chr10 135534747 7924108 0.05846550921735221 0.431228368474668 chr11 135006516 8878382 0.06576261845020873 0.46269910244410456 chr12 133851895 8909289 0.0665607984108107 0.31925913947226 chr13 115169878 5786159 0.050240211246902595 0.2624699730231035 chr14 107349540 6197016 0.05772745742552786 0.3426503335763739 chr15 102531392 5575081 0.05437438126266734 0.27650990197664216 chr16 90354753 5325353 0.05893827190253068 0.42769598463204617 chr17 81195210 4843566 0.059653346545935404 0.37359874828722195 chr18 78077248 5213517 0.06677383147520773 1.30927056172175 chr19 59128983 3588688 0.06069253719449225 0.7457227926803951 chr20 63025520 3511106 0.055709274592260404 0.29211909756789745 chr21 48129895 2421099 0.05030343407148509 0.3191731465980735 chr22 51304566 2086572 0.04067029823427412 0.233014626740186 chrMT 16571 21979 1.3263532677569247 1.4269768708518347 chrX 155270560 8961200 0.057713451925464815 0.3612962659858225 chrY 59373566 488649 0.008230076664083137 0.24770322711435655