BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504709.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,329,039 number of mapped reads = 2,108,531 (90.53%) number of secondary alignments = 0 number of mapped bases = 67,465,518 bp number of sequenced bases = 67,465,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,193 duplication rate = 8.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.0239 >>>>>>> ACTG content number of A's = 19,550,696 bp (28.98%) number of C's = 13,203,289 bp (19.57%) number of T's = 21,562,631 bp (31.96%) number of G's = 13,148,790 bp (19.49%) number of N's = 112 bp (0%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 35,896 >>>>>>> Coverage mean coverageData = 0.0218X std coverageData = 0.9828X There is a 1.09% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 6529922 0.02619821757635661 0.4518301973113873 chr2 243199373 5338028 0.021949184877215946 0.8191100386481207 chr3 198022430 4885582 0.02467186166738788 0.498899742708384 chr4 191154276 4518272 0.02363678226062806 0.32383566493412325 chr5 180915260 4155612 0.022969936311619043 0.2973583393241445 chr6 171115067 778526 0.0045497220884704445 0.11868728905932617 chr7 159138663 7734740 0.04860377644369175 3.506873056486533 chr8 146364022 3696456 0.025255222898971717 0.5111064667933333 chr9 141213431 3305170 0.023405493206945734 0.7350747376215393 chr10 135534747 3955116 0.02918156478353112 1.5147880191220378 chr11 135006516 620452 0.004595718920707501 0.12751861506365297 chr12 133851895 3411036 0.025483658636286023 1.0090799900157306 chr13 115169878 2435128 0.021143792476709927 0.34900298360321735 chr14 107349540 2217004 0.020652198416499967 0.6501049064871512 chr15 102531392 1389936 0.013556199451578693 0.19583626334844065 chr16 90354753 1058678 0.0117169043669457 0.17919727991422763 chr17 81195210 1284128 0.015815317184351144 0.255861980945416 chr18 78077248 1507468 0.01930739157199803 0.33831814384278175 chr19 59128983 213328 0.0036078415216443008 0.10537199760467976 chr20 63025520 965404 0.01531766814458651 0.23390481123959558 chr21 48129895 637228 0.01323975462651643 0.18481603681938175 chr22 51304566 107244 0.0020903402632818295 0.06090175006352643 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 6509104 0.041921044143848 0.717085950194673 chrY 59373566 211924 0.003569332520805639 0.11096508545061944