BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231823.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 = 762,505 number of mapped reads = 584,758 (76.69%) number of supplementary alignments = 5,224 (0.69%) number of secondary alignments = 0 number of mapped bases = 37,837,298 bp number of sequenced bases = 37,817,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,130 duplication rate = 5.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5095 >>>>>>> ACTG content number of A's = 10,630,586 bp (28.11%) number of C's = 6,260,916 bp (16.56%) number of T's = 12,853,960 bp (33.99%) number of G's = 8,069,823 bp (21.34%) number of N's = 1,888 bp (0%) GC percentage = 37.89% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 336,449 number of insertions = 3,496 mapped reads with insertion percentage = 0.59% number of deletions = 11,483 mapped reads with deletion percentage = 1.93% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.3545X There is a 1.03% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.03% 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 3309308 0.013277030110187769 0.20256229270505288 chr2 243199373 2643351 0.01086906996261047 0.14935683529398824 chr3 198022430 3919497 0.01979319716458383 0.1652048398898738 chr4 191154276 1425114 0.007455307983798385 0.1042168517014606 chr5 180915260 2478865 0.013701801605901016 0.14199163034116186 chr6 171115067 2168564 0.012673132986004091 0.13341444133723343 chr7 159138663 2312683 0.014532502387556191 0.16164280675531634 chr8 146364022 2384718 0.016293061419151218 1.4943270842255967 chr9 141213431 1460749 0.010344263924867033 0.12833130135906912 chr10 135534747 1463457 0.010797651763794564 0.13522072746920635 chr11 135006516 1495453 0.011076894984831696 0.135042725877661 chr12 133851895 1364772 0.01019613506405718 0.11706660181719931 chr13 115169878 1802883 0.015654119213358894 0.14788716625216808 chr14 107349540 1658565 0.01545013606951646 0.14707757233000382 chr15 102531392 778357 0.007591401860612601 0.09973596341134743 chr16 90354753 931375 0.010307980145770527 0.1226581138724655 chr17 81195210 891609 0.010981054177949659 0.12354937492566459 chr18 78077248 826172 0.01058146926490032 0.21926635154413449 chr19 59128983 904212 0.015292196045380993 0.1652888383151322 chr20 63025520 782746 0.012419508795802081 0.1322428480232124 chr21 48129895 669752 0.013915509269239004 0.13923663995912347 chr22 51304566 289976 0.005652050540686768 0.08350318441431967 chrMT 16571 47831 2.886428097278378 3.262869469992011 chrX 155270560 1700519 0.01095197312355929 0.12338069887541965 chrY 59373566 126770 0.002135125250856585 0.059968703127633215