BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080633.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 = 5,893,007 number of mapped reads = 4,829,840 (81.96%) number of supplementary alignments = 34,307 (0.58%) number of secondary alignments = 0 number of mapped bases = 319,251,953 bp number of sequenced bases = 319,116,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,485 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8249 >>>>>>> ACTG content number of A's = 86,799,372 bp (27.2%) number of C's = 56,509,940 bp (17.71%) number of T's = 104,032,398 bp (32.6%) number of G's = 71,515,502 bp (22.41%) number of N's = 259,063 bp (0.08%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,905,857 number of insertions = 27,381 mapped reads with insertion percentage = 0.56% number of deletions = 82,312 mapped reads with deletion percentage = 1.69% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.1031X std coverageData = 0.7928X There is a 8.14% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 39122220 0.1569593682175821 1.2937751702794058 chr2 243199373 24436162 0.10047789884721454 0.7149361862839713 chr3 198022430 21902714 0.11060723777604385 0.41116869377596393 chr4 191154276 14542090 0.07607514884992685 0.36315383085219527 chr5 180915260 18003935 0.09951584515313965 0.38436103501344815 chr6 171115067 20109441 0.11751999021804432 0.6225070784231655 chr7 159138663 18005190 0.11314151860129679 1.9833783035294856 chr8 146364022 20207286 0.13806183872154046 0.9848443152021163 chr9 141213431 12815203 0.09075059581266035 0.6315843601386042 chr10 135534747 14195427 0.10473644075935745 0.7606357614506666 chr11 135006516 15575852 0.11537111290243206 0.5943383535074367 chr12 133851895 12736698 0.09515515637638153 0.38515825634918255 chr13 115169878 7594786 0.06594420461225113 0.30360518340854586 chr14 107349540 8108129 0.07553016994763088 0.3983626705003701 chr15 102531392 8675226 0.08461043813781442 0.35108717386994454 chr16 90354753 7554674 0.08361125175119453 0.4211954819313672 chr17 81195210 8369884 0.10308347007169512 0.467224595204382 chr18 78077248 8871762 0.11362800594611122 1.1407042694427998 chr19 59128983 6443641 0.1089760160427586 0.8478608678013851 chr20 63025520 6860517 0.1088530011335091 0.4215957955731837 chr21 48129895 4332779 0.09002261484260458 0.4219732739737535 chr22 51304566 3360362 0.0654983028216241 0.30622362414932536 chrMT 16571 119123 7.188642809727837 6.817457185477096 chrX 155270560 16626179 0.10707875981126107 0.4576629994281873 chrY 59373566 682673 0.011497928219436912 0.23013965041959816