BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013180.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 = 1,218,682 number of mapped reads = 1,074,513 (88.17%) number of supplementary alignments = 9,257 (0.76%) number of secondary alignments = 0 number of mapped bases = 71,323,007 bp number of sequenced bases = 71,285,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,216 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7468 >>>>>>> ACTG content number of A's = 20,372,386 bp (28.58%) number of C's = 13,073,120 bp (18.34%) number of T's = 22,154,101 bp (31.08%) number of G's = 15,677,323 bp (21.99%) number of N's = 8,505 bp (0.01%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 590,990 number of insertions = 5,634 mapped reads with insertion percentage = 0.52% number of deletions = 21,678 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.2469X There is a 2.12% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 2566086 0.010295204038829657 0.23486571283386867 chr2 243199373 5790507 0.023809711877834486 0.3088250997014576 chr3 198022430 5627882 0.028420426918304154 0.1771592436149408 chr4 191154276 6934618 0.03627759810091823 0.2049400166501386 chr5 180915260 4341786 0.023999003732465687 0.16348579438152444 chr6 171115067 3850705 0.022503599872943977 0.20806942838539721 chr7 159138663 4725332 0.029693173933477122 0.38423171428562164 chr8 146364022 6300189 0.04304465615190597 0.4002989931496745 chr9 141213431 2621244 0.018562285339558105 0.25544133543688896 chr10 135534747 2992030 0.022075741211956518 0.2787656650572209 chr11 135006516 1911252 0.014156738923623508 0.18485701587548042 chr12 133851895 4510359 0.03369663910996553 0.19457592091842144 chr13 115169878 1737376 0.015085333336899081 0.12788596687011994 chr14 107349540 2962421 0.02759602882322551 0.1938465473859986 chr15 102531392 1126754 0.010989356313430329 0.11271936948438932 chr16 90354753 1997713 0.022109661458539983 0.1825874913751868 chr17 81195210 1660824 0.020454704162967248 0.17295481649969263 chr18 78077248 1238613 0.015863942847985625 0.5279629017356449 chr19 59128983 908138 0.015358593263814465 0.2462135995352983 chr20 63025520 1335470 0.021189353138220835 0.16530942871370394 chr21 48129895 1666368 0.03462230698820348 0.20486895916166972 chr22 51304566 473169 0.009222746373100593 0.10353856451982339 chrMT 16571 9522 0.5746183090942008 0.8097335494927986 chrX 155270560 3892222 0.025067353399124727 0.19664160536085673 chrY 59373566 142427 0.0023988284618107663 0.07431027413465528