BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004073.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 = 2,062,068 number of mapped reads = 1,835,510 (89.01%) number of supplementary alignments = 19,897 (0.96%) number of secondary alignments = 0 number of mapped bases = 122,873,533 bp number of sequenced bases = 122,828,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,013 duplication rate = 9.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3633 >>>>>>> ACTG content number of A's = 34,816,507 bp (28.35%) number of C's = 22,665,701 bp (18.45%) number of T's = 39,076,064 bp (31.81%) number of G's = 26,249,043 bp (21.37%) number of N's = 21,634 bp (0.02%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,101,163 number of insertions = 9,257 mapped reads with insertion percentage = 0.5% number of deletions = 25,838 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.5289X There is a 1.98% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 7868706 0.031569453943306326 0.6647666786835512 chr2 243199373 14750624 0.060652393211556514 0.7245456010843454 chr3 198022430 4591968 0.023189130645452638 0.25996876420223947 chr4 191154276 10272062 0.05373702443360461 0.41715451287214106 chr5 180915260 4295495 0.023743132558303816 0.2658667812300201 chr6 171115067 6788360 0.03967131661176277 0.3747612445089157 chr7 159138663 10199824 0.06409394051525995 1.0063005123402067 chr8 146364022 3660848 0.025011939067922033 0.6937911433590084 chr9 141213431 4963066 0.035145849547413094 0.5229374210140757 chr10 135534747 4285832 0.03162164754695709 0.33921213029984615 chr11 135006516 4831769 0.03578915405831227 0.3947434769005767 chr12 133851895 4165161 0.031117684213585472 0.31208204870375134 chr13 115169878 3131011 0.02718602341490715 0.2938073265544019 chr14 107349540 4979636 0.0463871200565927 0.39539636943223955 chr15 102531392 4077071 0.039764124142584546 0.345469195667506 chr16 90354753 3878795 0.04292851091076526 0.3837620550062485 chr17 81195210 2461242 0.030312650216681503 0.33906759707934264 chr18 78077248 6011125 0.07698945792761548 1.0857713108344842 chr19 59128983 1613445 0.02728687215878548 0.5022368129091908 chr20 63025520 3323909 0.05273909679761468 0.4226630896757067 chr21 48129895 3245005 0.06742181756266039 0.4628935040962079 chr22 51304566 888268 0.017313624678162175 0.2168426955696345 chrMT 16571 137840 8.318146158952386 6.409559261969576 chrX 155270560 8062014 0.0519223605556649 0.42404023659539203 chrY 59373566 390457 0.006576276722203278 0.17444415375552436