BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231759.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 = 6,148,898 number of mapped reads = 5,773,687 (93.9%) number of supplementary alignments = 29,295 (0.48%) number of secondary alignments = 0 number of mapped bases = 392,307,923 bp number of sequenced bases = 392,162,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 531,325 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8788 >>>>>>> ACTG content number of A's = 102,319,216 bp (26.09%) number of C's = 73,780,400 bp (18.81%) number of T's = 111,261,965 bp (28.37%) number of G's = 104,717,878 bp (26.7%) number of N's = 83,269 bp (0.02%) GC percentage = 45.52% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,635,502 number of insertions = 27,885 mapped reads with insertion percentage = 0.48% number of deletions = 88,202 mapped reads with deletion percentage = 1.51% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.1267X std coverageData = 35.9243X There is a 8.62% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% 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 0.01% 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 42959450 0.17235443517711435 1.7019171799192927 chr2 243199373 42788550 0.17594021510902497 128.1236081384748 chr3 198022430 33128598 0.1672971996152153 0.5424694370239707 chr4 191154276 7049274 0.03687740681249527 0.3200324922183156 chr5 180915260 22546026 0.12462202469819296 0.4787361986455088 chr6 171115067 32386655 0.18926828342941887 0.8317477482758955 chr7 159138663 26757285 0.1681381789666035 2.3213763367368387 chr8 146364022 23299632 0.15918961286811317 0.862922578229955 chr9 141213431 13718417 0.09714668713063136 0.9071668364404931 chr10 135534747 11250342 0.08300706829076089 0.7234625844817966 chr11 135006516 10821489 0.08015530894819921 0.8216502718009452 chr12 133851895 14070819 0.1051222995386057 0.44189430130136614 chr13 115169878 10181638 0.08840539016634193 0.3858298399789238 chr14 107349540 16629740 0.15491207507735943 0.7226019162817786 chr15 102531392 12127821 0.118283978822798 0.4700424820421435 chr16 90354753 11952345 0.13228241573522978 0.6469645108947808 chr17 81195210 11520816 0.1418903405755093 0.6216229277221413 chr18 78077248 7233957 0.09265128043447433 1.9559027952431765 chr19 59128983 10618370 0.17957978407983102 1.2601824917041544 chr20 63025520 9870466 0.1566106237600261 0.5598070588515693 chr21 48129895 9387199 0.19503884228295118 0.6824763338241491 chr22 51304566 3720353 0.07251504671143695 0.3532409216945151 chrMT 16571 13279 0.8013396898195643 1.1163287626673588 chrX 155270560 7543505 0.04858297026815644 0.4672419426395959 chrY 59373566 731897 0.012326984031917504 0.25752712161704183