BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525072.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 17,389,913 number of mapped reads = 16,148,646 (92.86%) number of supplementary alignments = 67,464 (0.39%) number of secondary alignments = 0 number of mapped bases = 953,923,056 bp number of sequenced bases = 953,652,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,942,571 duplication rate = 11.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0833 >>>>>>> ACTG content number of A's = 240,243,518 bp (25.19%) number of C's = 178,861,467 bp (18.76%) number of T's = 304,499,641 bp (31.93%) number of G's = 229,945,797 bp (24.11%) number of N's = 102,088 bp (0.01%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 4,236,513 number of insertions = 59,809 mapped reads with insertion percentage = 0.37% number of deletions = 166,687 mapped reads with deletion percentage = 1.02% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.3081X std coverageData = 1.9728X There is a 15.42% of reference with a coverageData >= 1X There is a 6.93% of reference with a coverageData >= 2X There is a 3.45% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 1% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 75742568 0.3038811606411203 3.967488596015114 chr2 243199373 80335459 0.33032757448762007 2.6156027794434786 chr3 198022430 64664341 0.32655058823386823 1.0349958586124854 chr4 191154276 62884738 0.3289737447463639 1.446695479563451 chr5 180915260 58418863 0.3229073268888429 1.020040139448202 chr6 171115067 54333530 0.31752627604674927 1.2176855286199844 chr7 159138663 53219595 0.33442278574377615 2.3617560690283246 chr8 146364022 47644621 0.32552139760138593 2.2243139646980983 chr9 141213431 39427932 0.27920808750833337 1.4749460532166063 chr10 135534747 46134189 0.340386432417954 2.3100176691620455 chr11 135006516 43317083 0.3208517950348411 1.5015204850884505 chr12 133851895 42733688 0.3192609861817795 1.0619087861177936 chr13 115169878 29825803 0.2589722548807423 0.9130407757076927 chr14 107349540 28851048 0.2687580030617737 0.9971713891703111 chr15 102531392 27924341 0.27234918453072404 0.9436705731046217 chr16 90354753 28185184 0.3119391406006057 1.231283454027098 chr17 81195210 24913459 0.30683409772571557 1.1375541286759479 chr18 78077248 25056868 0.32092406740565443 3.0772653922859488 chr19 59128983 19578746 0.331119275296854 2.6857166499607414 chr20 63025520 19907648 0.31586646171265226 1.1096859124623775 chr21 48129895 12823272 0.26643050021197845 1.2693042509569425 chr22 51304566 11340350 0.221039780357951 0.8532434190532451 chrMT 16571 444727 26.837668215557297 14.51061919762182 chrX 155270560 53175234 0.34246823093830536 1.337245068942283 chrY 59373566 3039769 0.05119734597042731 1.3961582856181134