BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504718.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 = 1,945,643 number of mapped reads = 1,727,251 (88.78%) number of secondary alignments = 0 number of mapped bases = 55,266,438 bp number of sequenced bases = 55,266,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,520 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.4875 >>>>>>> ACTG content number of A's = 16,161,188 bp (29.24%) number of C's = 10,950,243 bp (19.81%) number of T's = 17,026,016 bp (30.81%) number of G's = 11,128,924 bp (20.14%) number of N's = 67 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 31,522 >>>>>>> Coverage mean coverageData = 0.0179X std coverageData = 0.5483X There is a 1.3% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% 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% 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 4210460 0.016892475465487406 0.1944987788825567 chr2 243199373 4644380 0.019097006471311913 0.23134341820401993 chr3 198022430 5724972 0.02891072491131434 1.9249113942510256 chr4 191154276 3549830 0.018570497476080524 0.18013726183258616 chr5 180915260 3281750 0.01813970806000555 0.2151892398335773 chr6 171115067 3496160 0.020431631540663804 0.24088199391766763 chr7 159138663 2690234 0.016904967964950165 0.1893253734881676 chr8 146364022 2606894 0.017811030090441216 0.2057733968041964 chr9 141213431 2178486 0.015426903691618398 0.19047349357142096 chr10 135534747 2686736 0.01982322658557809 0.5762690358732081 chr11 135006516 2441814 0.0180866381293774 0.21398749395688885 chr12 133851895 2482164 0.01854410802327453 0.2041745772982804 chr13 115169878 1410074 0.012243427053035516 0.14021660083664023 chr14 107349540 1579826 0.014716653653103684 0.16376134793886402 chr15 102531392 1286000 0.01254250015448927 0.1407674538803825 chr16 90354753 1022048 0.011311502340114857 0.2196371161902598 chr17 81195210 896984 0.01104725266428894 0.13093491551744654 chr18 78077248 1190086 0.015242417355693684 0.16640147842465466 chr19 59128983 710376 0.012014006735072713 0.1939935110961778 chr20 63025520 1273324 0.020203308120266203 0.42972900173396517 chr21 48129895 549844 0.01142416786905519 0.13774658543040266 chr22 51304566 285686 0.005568432252209287 0.10685446213790095 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 4911428 0.03163141808724075 0.541984301544905 chrY 59373566 156850 0.002641748012912009 0.05749791870187692