BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080636.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 = 6,190,165 number of mapped reads = 5,033,647 (81.32%) number of supplementary alignments = 60,701 (0.98%) number of secondary alignments = 0 number of mapped bases = 337,222,506 bp number of sequenced bases = 337,090,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 457,439 duplication rate = 7.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0941 >>>>>>> ACTG content number of A's = 95,167,251 bp (28.23%) number of C's = 60,710,913 bp (18.01%) number of T's = 109,190,858 bp (32.39%) number of G's = 71,738,068 bp (21.28%) number of N's = 283,100 bp (0.08%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 3,074,449 number of insertions = 27,331 mapped reads with insertion percentage = 0.54% number of deletions = 81,462 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.66% >>>>>>> Coverage mean coverageData = 0.1089X std coverageData = 0.6238X There is a 6.75% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 41666183 0.1671658142027257 0.7879326038827171 chr2 243199373 19435869 0.07991743054370457 0.60490855918025 chr3 198022430 19360679 0.0977701313937012 0.456467134086236 chr4 191154276 16575435 0.0867123422339765 0.4381788837427191 chr5 180915260 16861367 0.09320035800186231 0.44496906741612485 chr6 171115067 19894137 0.11626174917723639 0.6405360958715709 chr7 159138663 21316232 0.13394753731216152 1.1421412661288872 chr8 146364022 40804962 0.2787909312850121 1.033552979095837 chr9 141213431 9738453 0.06896265412600873 0.4893168168558782 chr10 135534747 16319865 0.12041093049002408 0.6039437746238677 chr11 135006516 13730612 0.10170332815639802 0.5244249226630497 chr12 133851895 11483286 0.08579098562631482 0.4326691087411073 chr13 115169878 7113652 0.06176660185400214 0.36318492885783477 chr14 107349540 7460576 0.06949797828663262 0.409265314150147 chr15 102531392 6305657 0.06149976974856637 0.3677522415365762 chr16 90354753 9081831 0.10051304107931101 0.48128290487457953 chr17 81195210 5666360 0.0697868753587804 0.3964981688480101 chr18 78077248 8616392 0.1103572707890524 0.798624250081645 chr19 59128983 5440497 0.09201066421182992 0.6023887332411404 chr20 63025520 9103560 0.14444244172836654 0.5738163769025473 chr21 48129895 5629483 0.11696437318219788 0.5140776918020861 chr22 51304566 3316725 0.06464775474370059 0.36932513242495124 chrMT 16571 275941 16.652042725242893 26.344693143760097 chrX 155270560 21407415 0.13787169312714528 0.5676720389532829 chrY 59373566 617337 0.01039750585302557 0.16484213692410943