BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237820.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 = 3,468,109 number of mapped reads = 3,333,837 (96.13%) number of supplementary alignments = 49,433 (1.43%) number of secondary alignments = 0 number of mapped bases = 243,179,094 bp number of sequenced bases = 243,031,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,818 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1313 >>>>>>> ACTG content number of A's = 73,986,744 bp (30.44%) number of C's = 48,104,672 bp (19.79%) number of T's = 72,447,263 bp (29.81%) number of G's = 48,062,283 bp (19.78%) number of N's = 430,920 bp (0.18%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,202,283 number of insertions = 20,819 mapped reads with insertion percentage = 0.62% number of deletions = 80,093 mapped reads with deletion percentage = 2.37% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0786X std coverageData = 0.751X There is a 4.44% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.08% 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 0.01% 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 19445355 0.07801527202614271 1.4217261261282959 chr2 243199373 21290323 0.0875426722420045 0.8027937236349465 chr3 198022430 16262730 0.08212569656881799 0.4529671213262891 chr4 191154276 17399022 0.09102083596602359 0.6326546185192404 chr5 180915260 15294353 0.08453876693430946 0.4606379610941246 chr6 171115067 14076056 0.08226076316236956 0.5325890734563137 chr7 159138663 12837437 0.080668247162539 0.8329032461571991 chr8 146364022 12326730 0.08421967250940945 0.8011636277600006 chr9 141213431 9957190 0.070511635681453 0.7004659087732695 chr10 135534747 11110845 0.08197783406789404 0.910972546048027 chr11 135006516 11439746 0.08473476939438983 0.6797713868014719 chr12 133851895 11066382 0.08267631922581298 0.4640130067372873 chr13 115169878 7963049 0.06914176812794748 0.4151237473557631 chr14 107349540 7320086 0.06818926285105646 0.4435107197393289 chr15 102531392 7047358 0.06873366158922332 0.40973796568560084 chr16 90354753 6392584 0.07074983648065532 0.5120605464207029 chr17 81195210 5887984 0.07251639597951652 0.5620190987046692 chr18 78077248 6668792 0.08541274405573311 1.3416250177420168 chr19 59128983 3934024 0.06653292176528726 0.933047201458757 chr20 63025520 4875604 0.0773592030656788 0.4694863106164305 chr21 48129895 3322154 0.06902475062536496 0.5486927786942283 chr22 51304566 2374106 0.04627475067228909 0.3342168683394197 chrMT 16571 55343 3.3397501659525677 3.3257842490214014 chrX 155270560 13934719 0.08974475908375677 0.5319908856402967 chrY 59373566 897122 0.015109788083134505 0.6569385389487578