BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124976.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,887,262 number of mapped reads = 2,724,390 (94.36%) number of supplementary alignments = 9,613 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,385,392 number of mapped paired reads (second in pair) = 1,338,998 number of mapped paired reads (both in pair) = 2,662,242 number of mapped paired reads (singletons) = 62,148 number of mapped bases = 166,344,014 bp number of sequenced bases = 166,262,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,499 duplication rate = 4.19% >>>>>>> Insert size mean insert size = 71,119.004 std insert size = 2,490,242.5928 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 51.5732 >>>>>>> ACTG content number of A's = 46,648,162 bp (28.06%) number of C's = 29,338,307 bp (17.65%) number of T's = 50,028,981 bp (30.09%) number of G's = 40,246,786 bp (24.21%) number of N's = 0 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,317,403 number of insertions = 21,180 mapped reads with insertion percentage = 0.77% number of deletions = 51,467 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.6091X There is a 4.32% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 13178201 0.05287128652730618 0.4034264825956858 chr2 243199373 14722848 0.06053818239079095 0.6855988688939539 chr3 198022430 12010443 0.060651932207881704 0.3148145379651269 chr4 191154276 8414430 0.044019051920135964 0.5519938607076782 chr5 180915260 8992939 0.049708017996934035 0.2619900448913489 chr6 171115067 10012089 0.05851085573896307 0.32136129294488974 chr7 159138663 11039803 0.06937222414643511 0.48860295369624507 chr8 146364022 10133680 0.06923614055918742 0.33881609149789305 chr9 141213431 7030313 0.049785016554126496 0.3649719057748038 chr10 135534747 8194387 0.0604596768089293 1.9517998253544993 chr11 135006516 6377286 0.04723687558902712 0.29053803549289997 chr12 133851895 7608067 0.056839441832332666 0.2761513183259436 chr13 115169878 3945776 0.034260486062162886 0.2097836568140879 chr14 107349540 4577187 0.0426381612813618 0.2587377409313522 chr15 102531392 4554685 0.044422346280054405 0.24362505485720223 chr16 90354753 6720320 0.07437705020343534 1.0909499851063675 chr17 81195210 4205003 0.05178880626086194 0.36473960258082055 chr18 78077248 3224757 0.04130213452195446 0.489146820068003 chr19 59128983 2693009 0.045544652780515435 0.3573306800112096 chr20 63025520 3823372 0.06066387076219284 0.3296843547545302 chr21 48129895 2358310 0.0489988602717708 0.364271288766452 chr22 51304566 1634156 0.03185205776811366 0.22742701924163108 chrMT 16571 126491 7.63327499849134 5.298585391592676 chrX 155270560 7623637 0.04909905007105017 0.2882734966872662 chrY 59373566 3142825 0.0529330678908523 1.1651499902454658