BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3087918.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 = 1,860,912 number of mapped reads = 1,666,811 (89.57%) number of supplementary alignments = 15,744 (0.85%) number of secondary alignments = 0 number of mapped bases = 110,023,857 bp number of sequenced bases = 109,985,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,851 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.027 >>>>>>> ACTG content number of A's = 29,258,651 bp (26.6%) number of C's = 20,688,581 bp (18.81%) number of T's = 34,437,128 bp (31.31%) number of G's = 25,596,223 bp (23.27%) number of N's = 5,105 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 754,544 number of insertions = 7,689 mapped reads with insertion percentage = 0.46% number of deletions = 23,777 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.2931X There is a 2.93% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 10164336 0.040779581447863276 0.49023422490886387 chr2 243199373 10470256 0.04305215046750963 0.44136658624056957 chr3 198022430 9727783 0.04912465219217843 0.2663268187792449 chr4 191154276 4545004 0.02377662741899637 0.18408874075636505 chr5 180915260 5428180 0.030003991924174887 0.20394556584613446 chr6 171115067 6223882 0.03637249547405431 0.25822640483022274 chr7 159138663 9821015 0.061713569882134806 0.41817075600059184 chr8 146364022 8336462 0.05695704371939164 0.3053649788453698 chr9 141213431 4337100 0.030713084224970075 0.2307959861625592 chr10 135534747 4613628 0.034040186019604256 0.24256282561131332 chr11 135006516 4275569 0.031669352907381154 0.23816482683776247 chr12 133851895 4354502 0.03253224020474271 0.21249370585218316 chr13 115169878 3473120 0.030156496301923668 0.20435618802064928 chr14 107349540 2011205 0.018735105897985216 0.16052074170708971 chr15 102531392 2631308 0.025663437788887133 0.1973061286795385 chr16 90354753 2257023 0.024979571356915777 0.18842954462956377 chr17 81195210 2178781 0.02683386125856439 0.2035495025378349 chr18 78077248 4207468 0.05388852844813383 0.3518535522114474 chr19 59128983 3734724 0.06316232430380209 0.4078290643977744 chr20 63025520 1329221 0.02109020282577597 0.17121439295118343 chr21 48129895 1087690 0.02259905200291835 0.17811486714967192 chr22 51304566 652155 0.012711441706767386 0.13242154298078615 chrMT 16571 3795 0.22901454347957276 0.5741126396481293 chrX 155270560 3980532 0.025636102555436135 0.1950477054545484 chrY 59373566 179118 0.003016797070938943 0.06652213628820919