BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975336.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,285,660 number of mapped reads = 4,186,676 (97.69%) number of supplementary alignments = 24,502 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,091,305 number of mapped paired reads (second in pair) = 2,095,371 number of mapped paired reads (both in pair) = 4,154,014 number of mapped paired reads (singletons) = 32,662 number of mapped bases = 380,970,902 bp number of sequenced bases = 380,730,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,789 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 80,651.2658 std insert size = 2,677,383.3294 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.5784 >>>>>>> ACTG content number of A's = 112,379,668 bp (29.52%) number of C's = 72,170,003 bp (18.96%) number of T's = 116,719,643 bp (30.66%) number of G's = 79,454,023 bp (20.87%) number of N's = 7,427 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,977,032 number of insertions = 75,462 mapped reads with insertion percentage = 1.75% number of deletions = 128,738 mapped reads with deletion percentage = 3% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.1231X std coverageData = 1.582X There is a 8.54% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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% 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 29087687 0.11670055979519506 1.8049637103972567 chr2 243199373 34110636 0.1402579109445319 1.9663088596491047 chr3 198022430 22266828 0.11244598907305602 0.44891432638648404 chr4 191154276 26161780 0.1368621228227194 1.3855606612358318 chr5 180915260 23311149 0.1288512035966452 0.49278039212937497 chr6 171115067 33846455 0.19779938490162297 2.227367526998282 chr7 159138663 19912655 0.12512770073982588 1.5279508773977597 chr8 146364022 19093566 0.13045259168950687 0.6685834891110042 chr9 141213431 16008526 0.1133640467952372 2.505684765446204 chr10 135534747 19951462 0.14720551328435358 3.4006130351458967 chr11 135006516 17145248 0.12699570737756094 1.0544032003975368 chr12 133851895 16360008 0.12222470216054841 0.4499425749987955 chr13 115169878 11887500 0.10321709292771848 0.40262048007384715 chr14 107349540 10918884 0.10171337483141521 0.490633772830131 chr15 102531392 9953389 0.09707650316500141 0.39256870595065646 chr16 90354753 11309835 0.12517144504838612 1.735199722750725 chr17 81195210 7657727 0.09431254626966296 1.6432296864558626 chr18 78077248 15375976 0.19693286320747372 2.637825433258647 chr19 59128983 4496605 0.0760473928665406 1.0575813540032506 chr20 63025520 7130941 0.11314370750134231 0.5456812244150722 chr21 48129895 4810019 0.09993828160231806 0.656770420349746 chr22 51304566 3154475 0.06148526819230865 0.39031267169888095 chrMT 16571 73748 4.450425442037294 3.8976970314977764 chrX 155270560 11767702 0.07578836580482481 0.5773354091015247 chrY 59373566 5178101 0.08721222841828298 2.475116823059337