BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548994.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,870,292 number of mapped reads = 5,048,271 (86%) number of secondary alignments = 0 number of mapped bases = 200,553,670 bp number of sequenced bases = 200,532,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,571 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6671 >>>>>>> ACTG content number of A's = 61,036,935 bp (30.44%) number of C's = 39,349,799 bp (19.62%) number of T's = 59,727,769 bp (29.78%) number of G's = 40,416,425 bp (20.15%) number of N's = 1,553 bp (0%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 608,167 number of insertions = 5,603 mapped reads with insertion percentage = 0.11% number of deletions = 16,440 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0648X std coverageData = 0.6398X There is a 5.17% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% 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 16140191 0.064754867752165 0.8433304800415753 chr2 243199373 17554479 0.07218143198091222 0.40139875140282266 chr3 198022430 14354214 0.07248781867791441 0.3234415762741096 chr4 191154276 14058278 0.07354414609066867 0.3453508785902613 chr5 180915260 13003654 0.07187704342906176 0.3235971942620212 chr6 171115067 12184714 0.07120772129318104 0.3555366420354245 chr7 159138663 11322416 0.07114811565307672 0.5808048070267049 chr8 146364022 10532818 0.07196316318774022 2.174908196446394 chr9 141213431 8536953 0.060454256649284305 0.3625150397905615 chr10 135534747 9397479 0.06933630827524989 0.4284935206490365 chr11 135006516 9320872 0.06904016395771594 0.3790993351147106 chr12 133851895 9311859 0.06956837630128435 0.3252345723357457 chr13 115169878 6879660 0.05973489005519308 0.29107831703217935 chr14 107349540 6330564 0.05897150560682421 0.33334259078402495 chr15 102531392 5692266 0.05551729952130173 0.27933786781932435 chr16 90354753 5255664 0.05816698984280329 0.30842045855542377 chr17 81195210 4626287 0.05697733893415634 0.3060097435381433 chr18 78077248 5595587 0.0716673184997504 0.69661813808228 chr19 59128983 3211200 0.054308392214356196 0.6370606080321942 chr20 63025520 4056198 0.06435802513013776 0.3173199654320518 chr21 48129895 2632293 0.054691434502402304 0.320173859572097 chr22 51304566 1957045 0.038145630156972775 0.2460817163089857 chrMT 16571 4547 0.2743950274576067 0.6089730842793943 chrX 155270560 6703576 0.04317351595820869 0.28817149914267265 chrY 59373566 1890856 0.03184676493913133 0.37626877977490447