BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038426.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,645,748 number of mapped reads = 12,834,027 (94.05%) number of supplementary alignments = 252,584 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,494,783 number of mapped paired reads (second in pair) = 6,339,244 number of mapped paired reads (both in pair) = 12,656,800 number of mapped paired reads (singletons) = 177,227 number of mapped bases = 1,814,956,256 bp number of sequenced bases = 1,813,655,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,928,742 duplication rate = 8.53% >>>>>>> Insert size mean insert size = 92,500.5812 std insert size = 2,840,262.4078 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.5704 >>>>>>> ACTG content number of A's = 526,595,601 bp (29.04%) number of C's = 369,630,830 bp (20.38%) number of T's = 527,785,018 bp (29.1%) number of G's = 389,606,590 bp (21.48%) number of N's = 37,908 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 25,917,097 number of insertions = 327,370 mapped reads with insertion percentage = 2.41% number of deletions = 635,455 mapped reads with deletion percentage = 4.76% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.5863X std coverageData = 10.2086X There is a 26.76% of reference with a coverageData >= 1X There is a 13.08% of reference with a coverageData >= 2X There is a 6.29% of reference with a coverageData >= 3X There is a 3.35% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 0.99% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 112577216 0.4516627302605597 14.568172073173773 chr2 243199373 182831037 0.7517742942536287 11.296011101566089 chr3 198022430 115658696 0.5840686633327346 1.3174225772340271 chr4 191154276 104039538 0.5442700010540178 9.299816985220357 chr5 180915260 98316611 0.5434401221875922 1.2989642587021797 chr6 171115067 131050054 0.7658592331907277 16.406233666481462 chr7 159138663 126098595 0.7923818927648022 8.963213171512404 chr8 146364022 79612113 0.5439322581610937 2.3637558572207173 chr9 141213431 73115366 0.517764956790831 14.786610221575033 chr10 135534747 80328913 0.5926813217868035 21.943343774158684 chr11 135006516 105146000 0.7788216681334107 9.51934931729124 chr12 133851895 70612863 0.5275447389071332 1.1991144523834845 chr13 115169878 88702558 0.7701888683080831 1.50870150344933 chr14 107349540 32659557 0.30423564926314545 0.9901528741344388 chr15 102531392 31302961 0.30530123886350824 0.8470599621191149 chr16 90354753 73842647 0.8172524914101641 14.521995487063563 chr17 81195210 42637669 0.5251254230391177 8.274935596965234 chr18 78077248 28968770 0.3710270372234431 11.28984657818828 chr19 59128983 23543958 0.3981796541300228 8.141567447239836 chr20 63025520 67495524 1.0709237147111201 3.337285712025499 chr21 48129895 15407064 0.3201142242259203 3.9915396162097174 chr22 51304566 10922648 0.2128981658279694 0.7578352700373001 chrMT 16571 3061477 184.7490797175789 130.9567805370136 chrX 155270560 88937067 0.5727877003857009 2.348930094867064 chrY 59373566 28087354 0.4730615978161056 13.652350162759385