BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084827.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 = 1,962,926 number of mapped reads = 1,807,921 (92.1%) number of supplementary alignments = 18,370 (0.94%) number of secondary alignments = 0 number of mapped bases = 122,810,938 bp number of sequenced bases = 122,762,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,056 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.081 >>>>>>> ACTG content number of A's = 34,768,849 bp (28.32%) number of C's = 22,231,983 bp (18.11%) number of T's = 39,580,049 bp (32.24%) number of G's = 26,163,782 bp (21.31%) number of N's = 17,635 bp (0.01%) GC percentage = 39.42% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,003,692 number of insertions = 10,376 mapped reads with insertion percentage = 0.57% number of deletions = 29,686 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.96% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3641X There is a 3.33% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% 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 11130512 0.0446559047890998 0.5855838048772436 chr2 243199373 10724297 0.044096729640828475 0.49498279055017297 chr3 198022430 10728830 0.05417987245182276 0.2702703163965394 chr4 191154276 7439895 0.03892089235817042 0.230262786097375 chr5 180915260 6703479 0.03705314300186728 0.22920629158797526 chr6 171115067 7251509 0.042377968972188755 0.257292602363862 chr7 159138663 5960590 0.037455322846340615 0.35508912263575193 chr8 146364022 6859209 0.04686403739301452 0.605520975803622 chr9 141213431 7696729 0.05450422771754621 0.41591635035955016 chr10 135534747 4120440 0.030401355307063803 0.25119069130068816 chr11 135006516 5352985 0.03964982697575871 0.3245975697672266 chr12 133851895 5233604 0.03909996193927624 0.2346107225406643 chr13 115169878 3003092 0.026075325008158817 0.18531131628024372 chr14 107349540 2403808 0.02239234560297138 0.19059826718581796 chr15 102531392 3083721 0.030075871787637487 0.20832783447887587 chr16 90354753 1988490 0.022007586031473077 0.19428121305378782 chr17 81195210 2439213 0.030041341108668847 0.21536687654302722 chr18 78077248 5313693 0.06805686850028321 0.7295520225062514 chr19 59128983 1997713 0.03378568171889579 0.38948165643778326 chr20 63025520 2251635 0.03572576632449839 0.2283686773531633 chr21 48129895 1053432 0.021887269855876478 0.18368995336308944 chr22 51304566 979849 0.019098670477009784 0.15527053756250597 chrMT 16571 13335 0.8047190875626093 1.055021253455759 chrX 155270560 8798264 0.05666408364856802 0.3007414534587845 chrY 59373566 282614 0.0047599296966599584 0.1333141597624912