BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163013.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 102,798,974 number of mapped reads = 100,753,245 (98.01%) number of supplementary alignments = 743,405 (0.72%) number of secondary alignments = 0 number of mapped bases = 9,905,606,720 bp number of sequenced bases = 9,904,309,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,224,272 duplication rate = 45.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0266 >>>>>>> ACTG content number of A's = 2,421,532,151 bp (24.45%) number of C's = 2,531,269,406 bp (25.56%) number of T's = 2,414,942,458 bp (24.38%) number of G's = 2,534,260,189 bp (25.59%) number of N's = 2,305,700 bp (0.02%) GC percentage = 51.14% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 44,233,433 number of insertions = 688,799 mapped reads with insertion percentage = 0.67% number of deletions = 603,357 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 3.1998X std coverageData = 36.1471X There is a 14.35% of reference with a coverageData >= 1X There is a 8.45% of reference with a coverageData >= 2X There is a 5.82% of reference with a coverageData >= 3X There is a 5.02% of reference with a coverageData >= 4X There is a 4.48% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.93% of reference with a coverageData >= 7X There is a 3.74% of reference with a coverageData >= 8X There is a 3.58% of reference with a coverageData >= 9X There is a 3.44% of reference with a coverageData >= 10X There is a 3.32% of reference with a coverageData >= 11X There is a 3.21% of reference with a coverageData >= 12X There is a 3.11% of reference with a coverageData >= 13X There is a 3.02% of reference with a coverageData >= 14X There is a 2.93% of reference with a coverageData >= 15X There is a 2.85% of reference with a coverageData >= 16X There is a 2.77% of reference with a coverageData >= 17X There is a 2.7% of reference with a coverageData >= 18X There is a 2.63% of reference with a coverageData >= 19X There is a 2.57% of reference with a coverageData >= 20X There is a 2.51% of reference with a coverageData >= 21X There is a 2.45% of reference with a coverageData >= 22X There is a 2.4% of reference with a coverageData >= 23X There is a 2.35% of reference with a coverageData >= 24X There is a 2.3% of reference with a coverageData >= 25X There is a 2.25% of reference with a coverageData >= 26X There is a 2.2% of reference with a coverageData >= 27X There is a 2.16% of reference with a coverageData >= 28X There is a 2.11% of reference with a coverageData >= 29X There is a 2.07% of reference with a coverageData >= 30X There is a 2.03% of reference with a coverageData >= 31X There is a 1.99% of reference with a coverageData >= 32X There is a 1.96% of reference with a coverageData >= 33X There is a 1.92% of reference with a coverageData >= 34X There is a 1.89% of reference with a coverageData >= 35X There is a 1.85% of reference with a coverageData >= 36X There is a 1.82% of reference with a coverageData >= 37X There is a 1.79% of reference with a coverageData >= 38X There is a 1.76% of reference with a coverageData >= 39X There is a 1.73% of reference with a coverageData >= 40X There is a 1.7% of reference with a coverageData >= 41X There is a 1.67% of reference with a coverageData >= 42X There is a 1.64% of reference with a coverageData >= 43X There is a 1.61% of reference with a coverageData >= 44X There is a 1.59% of reference with a coverageData >= 45X There is a 1.56% of reference with a coverageData >= 46X There is a 1.54% of reference with a coverageData >= 47X There is a 1.51% of reference with a coverageData >= 48X There is a 1.49% of reference with a coverageData >= 49X There is a 1.47% of reference with a coverageData >= 50X There is a 1.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1499555671 6.01625650914627 53.444960356050544 chr2 243199373 427687951 1.7585898587000057 18.63420081085939 chr3 198022430 426813171 2.155377908452088 20.677899037093606 chr4 191154276 219177145 1.1465981802049774 18.501512080118953 chr5 180915260 540277382 2.9863560542101313 42.477409878544265 chr6 171115067 574162164 3.3554155929471716 31.71757084512392 chr7 159138663 645720332 4.057595557403923 51.3992640749612 chr8 146364022 494143642 3.3761277891092663 56.19071175601116 chr9 141213431 262402298 1.8581964629129364 19.189170880381077 chr10 135534747 229329292 1.6920332023787228 16.84592907100877 chr11 135006516 553618311 4.100678451697842 32.53047501089789 chr12 133851895 288080000 2.152229522040013 20.546268544630998 chr13 115169878 142780604 1.239739126926921 15.348053386377403 chr14 107349540 306685893 2.85689061173434 25.526895364245764 chr15 102531392 448621990 4.375459859161963 33.89815711124063 chr16 90354753 439681540 4.866169464267142 35.91715395080754 chr17 81195210 294415945 3.6260260303532683 28.587285939550625 chr18 78077248 176638253 2.262352446131298 23.04527634353915 chr19 59128983 832652389 14.08196702791252 89.42458394022572 chr20 63025520 258015659 4.093828325414848 33.2411642283231 chr21 48129895 146893900 3.0520303441343475 66.04125910984291 chr22 51304566 126492506 2.465521411875894 20.626482707595073 chrMT 16571 6078 0.36678534789692835 0.8478721197583683 chrX 155270560 560183096 3.6077869236769673 35.36076162757902 chrY 59373566 11571508 0.19489326276949578 10.651188053986463