BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008819.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,375,690 number of mapped reads = 1,090,699 (79.28%) number of supplementary alignments = 12,740 (0.93%) number of secondary alignments = 0 number of mapped bases = 74,393,085 bp number of sequenced bases = 74,346,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,104 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9161 >>>>>>> ACTG content number of A's = 23,338,937 bp (31.39%) number of C's = 13,409,557 bp (18.04%) number of T's = 21,996,372 bp (29.59%) number of G's = 15,575,342 bp (20.95%) number of N's = 26,072 bp (0.04%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 721,237 number of insertions = 5,143 mapped reads with insertion percentage = 0.47% number of deletions = 29,172 mapped reads with deletion percentage = 2.64% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2141X There is a 2.04% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.05% 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 6219570 0.02495307724830102 0.3116698742301701 chr2 243199373 7077847 0.02910306434054828 0.22260338425468348 chr3 198022430 9454613 0.04774516200008252 0.2555865093833722 chr4 191154276 4206562 0.022006109871170236 0.17057882109914557 chr5 180915260 4076937 0.022535064206302996 0.1707618634665728 chr6 171115067 2982275 0.01742847694411387 0.17574753620415365 chr7 159138663 4100495 0.025766805644207278 0.2673726158680918 chr8 146364022 9622969 0.06574681993912411 0.34789574963034137 chr9 141213431 1028742 0.007285015261756511 0.10856140874374055 chr10 135534747 4499798 0.03320032758831947 0.29764489956924634 chr11 135006516 2572356 0.019053569236613735 0.17417095149712702 chr12 133851895 4193754 0.03133130091284849 0.20308874531109597 chr13 115169878 1291758 0.011216109823438382 0.12280282874244684 chr14 107349540 3395541 0.03163069911617693 0.20518891654370944 chr15 102531392 530634 0.00517533205830269 0.07935145946187361 chr16 90354753 2959033 0.032749057484557566 0.23053463256631102 chr17 81195210 943957 0.011625772012905688 0.13934781166566984 chr18 78077248 553600 0.007090413842455103 0.16925339381786564 chr19 59128983 542337 0.00917210093060454 0.2099812727948748 chr20 63025520 725022 0.011503625832837238 0.12099698251340507 chr21 48129895 317789 0.0066027361996114885 0.0910765488557069 chr22 51304566 237258 0.0046245006730979855 0.07449329688647113 chrMT 16571 10347 0.624404079415847 0.9573703201220705 chrX 155270560 2725712 0.01755459631239818 0.15430762822397703 chrY 59373566 124179 0.0020914863021702285 0.0518663070104409