BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006449.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,222,940 number of mapped reads = 1,139,826 (93.2%) number of supplementary alignments = 3,431 (0.28%) number of secondary alignments = 0 number of mapped bases = 62,696,301 bp number of sequenced bases = 62,677,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,204 duplication rate = 0.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3093 >>>>>>> ACTG content number of A's = 17,941,103 bp (28.62%) number of C's = 13,137,454 bp (20.96%) number of T's = 17,954,870 bp (28.65%) number of G's = 13,643,264 bp (21.77%) number of N's = 1,178 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 255,739 number of insertions = 3,887 mapped reads with insertion percentage = 0.34% number of deletions = 11,299 mapped reads with deletion percentage = 0.99% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.1901X There is a 1.91% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4919249 0.019736155441715027 0.26072048368386463 chr2 243199373 5521017 0.022701608692058593 0.17752332518569633 chr3 198022430 4124843 0.02083018070225681 0.1494117808993866 chr4 191154276 4321396 0.022606849767776056 0.1598233198369057 chr5 180915260 3880136 0.021447256577471686 0.15210782057302671 chr6 171115067 3672517 0.021462265505818957 0.15853326972125212 chr7 159138663 3652319 0.02295054470829631 0.20573188825038322 chr8 146364022 3283128 0.022431250215302227 0.39214135422462326 chr9 141213431 2512196 0.01779006417597771 0.1524637204852701 chr10 135534747 3179253 0.02345710653814848 0.20748907242619666 chr11 135006516 2813116 0.02083689056904483 0.1635946026746704 chr12 133851895 2940410 0.02196763818696777 0.1540033821164871 chr13 115169878 2139422 0.018576228760092982 0.1407614320873486 chr14 107349540 1943255 0.01810212693971488 0.14215062426572309 chr15 102531392 1753457 0.01710165994820396 0.13564437052111067 chr16 90354753 1776423 0.019660537393090986 0.15929013967334202 chr17 81195210 1797146 0.0221336455685009 0.16381775405294408 chr18 78077248 1359416 0.017411166950966304 0.20184457903727487 chr19 59128983 1294975 0.02190085021418346 0.22523678154937188 chr20 63025520 1407236 0.022328034738943844 0.15637988575075012 chr21 48129895 1118237 0.023233730304211136 0.16368605571464204 chr22 51304566 807931 0.015747740659184214 0.13678803371176257 chrMT 16571 64635 3.9004888057449763 2.4465625907150375 chrX 155270560 1912159 0.01231501322594573 0.11897682102590552 chrY 59373566 502429 0.008462166479944964 0.12850392460442162