BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618565.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 268,487,462 number of mapped reads = 257,388,436 (95.87%) number of supplementary alignments = 2,930,541 (1.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 129,449,019 number of mapped paired reads (second in pair) = 127,939,417 number of mapped paired reads (both in pair) = 253,641,308 number of mapped paired reads (singletons) = 3,747,128 number of mapped bases = 24,188,933,165 bp number of sequenced bases = 24,172,524,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,734,606 duplication rate = 31.7% >>>>>>> Insert size mean insert size = 141,209.4429 std insert size = 3,760,694.0527 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 52.3296 >>>>>>> ACTG content number of A's = 6,444,031,698 bp (26.66%) number of C's = 5,398,181,770 bp (22.33%) number of T's = 6,499,078,322 bp (26.89%) number of G's = 5,829,621,032 bp (24.12%) number of N's = 1,612,006 bp (0.01%) GC percentage = 46.45% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 331,110,282 number of insertions = 4,069,178 mapped reads with insertion percentage = 1.56% number of deletions = 11,868,053 mapped reads with deletion percentage = 4.5% homopolymer indels = 51.97% >>>>>>> Coverage mean coverageData = 7.8137X std coverageData = 28.995X There is a 44.31% of reference with a coverageData >= 1X There is a 36.61% of reference with a coverageData >= 2X There is a 31.67% of reference with a coverageData >= 3X There is a 28.16% of reference with a coverageData >= 4X There is a 25.4% of reference with a coverageData >= 5X There is a 23.18% of reference with a coverageData >= 6X There is a 21.32% of reference with a coverageData >= 7X There is a 19.74% of reference with a coverageData >= 8X There is a 18.37% of reference with a coverageData >= 9X There is a 17.17% of reference with a coverageData >= 10X There is a 16.11% of reference with a coverageData >= 11X There is a 15.16% of reference with a coverageData >= 12X There is a 14.31% of reference with a coverageData >= 13X There is a 13.54% of reference with a coverageData >= 14X There is a 12.84% of reference with a coverageData >= 15X There is a 12.2% of reference with a coverageData >= 16X There is a 11.61% of reference with a coverageData >= 17X There is a 11.07% of reference with a coverageData >= 18X There is a 10.57% of reference with a coverageData >= 19X There is a 10.11% of reference with a coverageData >= 20X There is a 9.67% of reference with a coverageData >= 21X There is a 9.27% of reference with a coverageData >= 22X There is a 8.89% of reference with a coverageData >= 23X There is a 8.54% of reference with a coverageData >= 24X There is a 8.21% of reference with a coverageData >= 25X There is a 7.9% of reference with a coverageData >= 26X There is a 7.61% of reference with a coverageData >= 27X There is a 7.33% of reference with a coverageData >= 28X There is a 7.07% of reference with a coverageData >= 29X There is a 6.82% of reference with a coverageData >= 30X There is a 6.59% of reference with a coverageData >= 31X There is a 6.37% of reference with a coverageData >= 32X There is a 6.16% of reference with a coverageData >= 33X There is a 5.95% of reference with a coverageData >= 34X There is a 5.76% of reference with a coverageData >= 35X There is a 5.58% of reference with a coverageData >= 36X There is a 5.41% of reference with a coverageData >= 37X There is a 5.24% of reference with a coverageData >= 38X There is a 5.08% of reference with a coverageData >= 39X There is a 4.93% of reference with a coverageData >= 40X There is a 4.79% of reference with a coverageData >= 41X There is a 4.65% of reference with a coverageData >= 42X There is a 4.51% of reference with a coverageData >= 43X There is a 4.39% of reference with a coverageData >= 44X There is a 4.26% of reference with a coverageData >= 45X There is a 4.15% of reference with a coverageData >= 46X There is a 4.03% of reference with a coverageData >= 47X There is a 3.92% of reference with a coverageData >= 48X There is a 3.82% of reference with a coverageData >= 49X There is a 3.72% of reference with a coverageData >= 50X There is a 3.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2338210978 9.380963500187228 37.32094528341917 chr2 243199373 2149176920 8.83709893446148 32.810216380058684 chr3 198022430 1591390465 8.036415192965766 23.741700473580003 chr4 191154276 1250009052 6.539268062201235 25.322706867605827 chr5 180915260 1401634993 7.7474669245701 23.723882844563068 chr6 171115067 1363431026 7.967919189722784 24.60071801563088 chr7 159138663 1212811145 7.6210967349901635 23.97417577387456 chr8 146364022 1187399518 8.112646139226756 24.631010664458433 chr9 141213431 1101862938 7.802819676550455 31.336368290894374 chr10 135534747 1307311765 9.645583836888706 29.235559608238656 chr11 135006516 1215464529 9.003006410446144 32.34776501416901 chr12 133851895 1130077872 8.442748397398482 25.336071936696904 chr13 115169878 650568162 5.648770088998445 18.656087544916385 chr14 107349540 776955317 7.237621297678593 25.8597031168363 chr15 102531392 816989066 7.968184670700658 26.388348267160733 chr16 90354753 907816184 10.04724327009117 45.595641400142064 chr17 81195210 845549452 10.413784901843348 32.839682740935714 chr18 78077248 644829926 8.258871086235006 32.57686080563617 chr19 59128983 488159750 8.25584553010154 30.92019999862583 chr20 63025520 725426446 11.5100430111485 34.44033112957907 chr21 48129895 333100738 6.920869825292575 46.52381857513547 chr22 51304566 452611301 8.822047164379093 32.63041389186694 chrMT 16571 30159 1.8199867237945808 6.442175636300274 chrX 155270560 51501813 0.3316907789860486 5.775585631186931 chrY 59373566 246613650 4.153593368469733 26.379779072822757