BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231773.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 542,498 number of mapped reads = 363,369 (66.98%) number of supplementary alignments = 3,117 (0.57%) number of secondary alignments = 0 number of mapped bases = 24,360,932 bp number of sequenced bases = 24,347,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,283 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3077 >>>>>>> ACTG content number of A's = 7,041,860 bp (28.92%) number of C's = 4,258,685 bp (17.49%) number of T's = 7,930,992 bp (32.57%) number of G's = 5,114,454 bp (21.01%) number of N's = 1,281 bp (0.01%) GC percentage = 38.5% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 211,762 number of insertions = 2,244 mapped reads with insertion percentage = 0.61% number of deletions = 7,876 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1122X There is a 0.73% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 1487046 0.0059660673824359295 0.13649834545372527 chr2 243199373 2254037 0.009268268138174846 0.11688721023457024 chr3 198022430 2330309 0.011767904272258451 0.11452554291523703 chr4 191154276 1047680 0.005480808600902027 0.08143878753992556 chr5 180915260 1219632 0.006741454535123239 0.0870899043459392 chr6 171115067 1757358 0.010270036594731895 0.11314442366469589 chr7 159138663 1271765 0.007991552624769757 0.11128851877701088 chr8 146364022 1231184 0.00841179398581982 0.20557681596081404 chr9 141213431 1566416 0.011092542606658994 0.12035332692077785 chr10 135534747 1228200 0.009061882854291232 0.10906440442154894 chr11 135006516 1143956 0.008473339168310957 0.10394196790448995 chr12 133851895 796430 0.005950083859477671 0.082961597680254 chr13 115169878 808300 0.007018328177789682 0.08864304690136608 chr14 107349540 821592 0.007653428230805647 0.09380953629757466 chr15 102531392 531850 0.005187191840719377 0.07738627162812786 chr16 90354753 476270 0.005271111747712929 0.0782145168331937 chr17 81195210 404487 0.0049816608639844644 0.07675913217109555 chr18 78077248 507706 0.00650261136253163 0.14593051329919035 chr19 59128983 333616 0.005642173821930947 0.09646726493431416 chr20 63025520 780916 0.01239047293858107 0.11897487463978218 chr21 48129895 598920 0.012443825194299717 0.12003348454164903 chr22 51304566 172667 0.0033655289082846936 0.06104922643570151 chrMT 16571 19908 1.2013758976525255 1.2898934141183607 chrX 155270560 1501682 0.009671389090114701 0.1059040871010372 chrY 59373566 69005 0.001162217543072956 0.04256919194120466