BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238054.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 = 1,970,622 number of mapped reads = 1,772,443 (89.94%) number of supplementary alignments = 18,743 (0.95%) number of secondary alignments = 0 number of mapped bases = 118,361,094 bp number of sequenced bases = 118,302,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,360 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5149 >>>>>>> ACTG content number of A's = 32,169,036 bp (27.19%) number of C's = 22,772,520 bp (19.25%) number of T's = 36,572,795 bp (30.91%) number of G's = 26,771,943 bp (22.63%) number of N's = 15,999 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 907,802 number of insertions = 8,247 mapped reads with insertion percentage = 0.46% number of deletions = 33,182 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3217X There is a 3.09% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 4826089 0.019362395089077833 0.44322252399449535 chr2 243199373 6227065 0.02560477407151868 0.34491752432041106 chr3 198022430 3704445 0.01870719897740877 0.15996394540568837 chr4 191154276 4740016 0.024796808625928934 0.1978589997907964 chr5 180915260 8998439 0.049738418970295815 0.2661887172646395 chr6 171115067 2740595 0.01601609401234083 0.20899924026086963 chr7 159138663 4805290 0.030195616259513253 0.2310066774942604 chr8 146364022 13400019 0.0915526836233019 0.5864737495067862 chr9 141213431 2855344 0.020220059662738453 0.24279371550210885 chr10 135534747 10568620 0.07797719945572333 0.3772443848381412 chr11 135006516 3262567 0.024165996550862774 0.26407947726699504 chr12 133851895 7906660 0.05907021338771483 0.2904697103309154 chr13 115169878 3149207 0.027344016115047026 0.19408076013057943 chr14 107349540 6535889 0.06088418264298105 0.30036751058140393 chr15 102531392 4657519 0.045425297649328705 0.2536301499943481 chr16 90354753 4515398 0.04997410595544431 0.29854659478595685 chr17 81195210 5571563 0.06861935574770975 0.41164887262763766 chr18 78077248 3575928 0.04579987245452094 0.5753057370565734 chr19 59128983 2690255 0.04549807663696837 0.4134709499590728 chr20 63025520 2709876 0.042996487771937465 0.25346397796419884 chr21 48129895 3356461 0.06973755085067192 0.32588693765797677 chr22 51304566 1146842 0.022353604940347806 0.1769106113746668 chrMT 16571 59891 3.614205539798443 2.970084105303682 chrX 155270560 6042722 0.038917371071502546 0.254791145705546 chrY 59373566 314394 0.005295184729177291 0.15318233783759047