BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013252.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 = 1,716,790 number of mapped reads = 1,343,674 (78.27%) number of supplementary alignments = 9,948 (0.58%) number of secondary alignments = 0 number of mapped bases = 86,076,981 bp number of sequenced bases = 86,040,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,695 duplication rate = 6.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2282 >>>>>>> ACTG content number of A's = 22,315,401 bp (25.94%) number of C's = 15,925,062 bp (18.51%) number of T's = 27,261,639 bp (31.68%) number of G's = 20,537,390 bp (23.87%) number of N's = 1,145 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 662,087 number of insertions = 5,320 mapped reads with insertion percentage = 0.39% number of deletions = 20,946 mapped reads with deletion percentage = 1.54% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0278X std coverageData = 0.2654X There is a 2.07% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7377144 0.029597294363411034 0.3241637934600497 chr2 243199373 14207980 0.05842112101168945 0.43207785599251974 chr3 198022430 5486646 0.02770719458396708 0.2136319973163335 chr4 191154276 4816541 0.02519713971765926 0.2067786619634909 chr5 180915260 3757420 0.02076895005982359 0.1852850566225001 chr6 171115067 4646072 0.02715174111465006 0.2407023355205342 chr7 159138663 5331266 0.0335007590204525 0.436956495989374 chr8 146364022 3778624 0.025816617693110402 0.2423205387515295 chr9 141213431 3070955 0.021746904513636527 0.21519709939392972 chr10 135534747 3267538 0.024108489316027572 0.22351377915135195 chr11 135006516 3477243 0.025756112393864012 0.2441106939681904 chr12 133851895 3332490 0.024896845875809228 0.20315583333766637 chr13 115169878 1625642 0.014115166467398707 0.15167873621938593 chr14 107349540 2616988 0.024378194820396996 0.2065690656641027 chr15 102531392 2334304 0.022766724946053595 0.19679382717683125 chr16 90354753 2863088 0.0316871875019126 0.23230948390100445 chr17 81195210 2144007 0.026405584762943527 0.22066825571078885 chr18 78077248 1804320 0.023109421069759016 0.29847351284277 chr19 59128983 1464535 0.024768479444336123 0.25814129423269877 chr20 63025520 1884907 0.029907044003762286 0.2240973628905028 chr21 48129895 1108695 0.023035475144917727 0.19840786598704038 chr22 51304566 840431 0.016381212541589377 0.16245283765751029 chrMT 16571 23836 1.4384165107718303 1.6550596970033578 chrX 155270560 4645784 0.029920572193466683 0.24392128259413334 chrY 59373566 170525 0.0028720693650100115 0.07184267183398904