BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236123.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 = 1,511,964 number of mapped reads = 1,280,536 (84.69%) number of supplementary alignments = 10,023 (0.66%) number of secondary alignments = 0 number of mapped bases = 83,494,752 bp number of sequenced bases = 83,454,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,389 duplication rate = 4.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2227 >>>>>>> ACTG content number of A's = 22,705,120 bp (27.21%) number of C's = 14,784,439 bp (17.72%) number of T's = 27,154,611 bp (32.54%) number of G's = 18,768,675 bp (22.49%) number of N's = 41,255 bp (0.05%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 696,154 number of insertions = 6,132 mapped reads with insertion percentage = 0.48% number of deletions = 23,351 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2969X There is a 2.22% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 6055082 0.024293147097113953 0.539843209171544 chr2 243199373 5149866 0.02117549044832447 0.2863231057474878 chr3 198022430 6023396 0.03041774611088249 0.20308096767049771 chr4 191154276 6254989 0.03272220287659168 0.24211727962924717 chr5 180915260 7340375 0.040573553607362915 0.2369594827675554 chr6 171115067 7056100 0.04123599472394795 0.2976309675331744 chr7 159138663 3725554 0.023410740858115668 0.313982242659673 chr8 146364022 5635154 0.03850095073227763 0.48569910891435397 chr9 141213431 3674533 0.026021129675689276 0.26216196812647374 chr10 135534747 1951463 0.014398248738384408 0.240778938589812 chr11 135006516 2506935 0.018568992625511496 0.1994457629362735 chr12 133851895 1617719 0.012085887913652624 0.1337021937710047 chr13 115169878 2831880 0.02458872101957076 0.1831024510312895 chr14 107349540 3910872 0.03643119476804465 0.23240453397645952 chr15 102531392 2286604 0.022301501573293768 0.17855964706282113 chr16 90354753 2899950 0.03209515718558823 0.2198031307667909 chr17 81195210 2908594 0.035822236311723314 0.26843865305057485 chr18 78077248 1975136 0.025297203098141985 0.4177910966552555 chr19 59128983 2256631 0.038164549523877316 0.4162600641752908 chr20 63025520 1168322 0.018537284579325963 0.16487718404135934 chr21 48129895 600213 0.012470689994233314 0.15577467110855567 chr22 51304566 887059 0.017290059524136703 0.15104142037402576 chrMT 16571 101720 6.138434614688311 4.6121366751606665 chrX 155270560 4463862 0.028748927034204036 0.20924808175264833 chrY 59373566 212743 0.003583126538163465 0.12355428714480375