BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,355,138 number of mapped reads = 3,293,912 (98.18%) number of supplementary alignments = 75,627 (2.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,660,466 number of mapped paired reads (second in pair) = 1,633,446 number of mapped paired reads (both in pair) = 3,264,196 number of mapped paired reads (singletons) = 29,716 number of mapped bases = 416,990,859 bp number of sequenced bases = 416,636,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 651,493 duplication rate = 16.82% >>>>>>> Insert size mean insert size = 86,499.6072 std insert size = 2,757,748.8871 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.2515 >>>>>>> ACTG content number of A's = 120,731,298 bp (28.98%) number of C's = 82,598,433 bp (19.83%) number of T's = 122,588,228 bp (29.42%) number of G's = 90,715,376 bp (21.77%) number of N's = 3,202 bp (0%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 4,645,514 number of insertions = 89,647 mapped reads with insertion percentage = 2.53% number of deletions = 163,779 mapped reads with deletion percentage = 4.75% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.1347X std coverageData = 2.0852X There is a 7.24% of reference with a coverageData >= 1X There is a 3.54% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 36476576 0.14634497540529698 1.8131933464659928 chr2 243199373 36158537 0.14867857821327524 2.2285844196455264 chr3 198022430 29682698 0.14989563556007265 0.6151160366164888 chr4 191154276 22234275 0.11631586520199004 2.026416256602034 chr5 180915260 23462062 0.1296853676135446 0.5623947416948352 chr6 171115067 21154374 0.12362660033905723 0.8388034543963585 chr7 159138663 29488922 0.18530331626576504 1.7966170397370984 chr8 146364022 28119134 0.1921178006436582 0.856698329690958 chr9 141213431 16232134 0.11494752223674815 2.0905547894029795 chr10 135534747 22992786 0.16964495458865614 6.831055822086588 chr11 135006516 14613807 0.108245197587352 0.7937188131249789 chr12 133851895 20056348 0.149839850978576 0.5823996396987721 chr13 115169878 10383067 0.0901543631052557 0.44270333652657473 chr14 107349540 12228107 0.1139092631416958 0.5477157967979258 chr15 102531392 10236432 0.09983705283158548 0.4741077922071462 chr16 90354753 15542006 0.1720109400332266 3.116577641271311 chr17 81195210 8588737 0.10577886306347382 1.656648383165032 chr18 78077248 6617341 0.08475376847298716 2.0331616654908164 chr19 59128983 6273029 0.10609059519931198 1.078370851767817 chr20 63025520 8446770 0.1340214249719796 0.8710608138110819 chr21 48129895 4486718 0.09322102198643899 1.1360212429620482 chr22 51304566 3483373 0.06789596465936384 0.4432976808846999 chrMT 16571 343358 20.72041518315129 12.43111570177079 chrX 155270560 20676531 0.13316452906462115 0.6977496174033022 chrY 59373566 9013737 0.1518139739155974 3.9456975165196106