BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975264.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 = 11,649,790 number of mapped reads = 11,505,539 (98.76%) number of supplementary alignments = 72,082 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,756,966 number of mapped paired reads (second in pair) = 5,748,573 number of mapped paired reads (both in pair) = 11,467,778 number of mapped paired reads (singletons) = 37,761 number of mapped bases = 1,042,565,236 bp number of sequenced bases = 1,041,975,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 695,757 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 72,384.1668 std insert size = 2,579,619.8638 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.6738 >>>>>>> ACTG content number of A's = 302,446,363 bp (29.03%) number of C's = 209,348,788 bp (20.09%) number of T's = 303,237,630 bp (29.1%) number of G's = 226,932,518 bp (21.78%) number of N's = 10,037 bp (0%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 7,800,570 number of insertions = 167,460 mapped reads with insertion percentage = 1.42% number of deletions = 358,726 mapped reads with deletion percentage = 3.06% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 0.3368X std coverageData = 2.7254X There is a 19.07% of reference with a coverageData >= 1X There is a 7.85% of reference with a coverageData >= 2X There is a 2.99% of reference with a coverageData >= 3X There is a 1.3% of reference with a coverageData >= 4X There is a 0.59% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% 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 72020107 0.2889465499064895 3.214329887531399 chr2 243199373 85782481 0.3527249266386883 3.6498080543280658 chr3 198022430 65221263 0.32936300700885246 0.8723668329561121 chr4 191154276 57805881 0.3024043312533589 1.8077606772302928 chr5 180915260 76768519 0.42433412748045685 0.9791761737833562 chr6 171115067 55338290 0.32339811432268556 1.9762754735616868 chr7 159138663 73699046 0.463112135106979 3.4673808661555787 chr8 146364022 79889102 0.5458247246034275 1.8359663247111995 chr9 141213431 35415494 0.2507940905422799 4.870834267128195 chr10 135534747 51206705 0.37781237751526553 4.745736447473202 chr11 135006516 54626380 0.4046203221776347 2.265679348723387 chr12 133851895 49335794 0.368584949805903 0.9123940943210154 chr13 115169878 14249783 0.12372838495148879 0.4758853173407724 chr14 107349540 28756969 0.26788162296736434 0.8620251284155498 chr15 102531392 24271292 0.23672059382554758 0.7004383659694109 chr16 90354753 37991307 0.4204682735395226 4.455345615062389 chr17 81195210 28712847 0.35362735067745993 3.6368994959860435 chr18 78077248 22155010 0.2837575678896879 4.834191768364475 chr19 59128983 12832695 0.21702884691928492 1.991675724975271 chr20 63025520 22041738 0.34972718987483165 0.9618108642546963 chr21 48129895 12128513 0.25199541781672286 1.0861432494097845 chr22 51304566 10890459 0.21227075578419277 0.7250348680323093 chrMT 16571 1281061 77.30740450184057 38.03808386429897 chrX 155270560 67828750 0.43684230932122614 1.568595024346932 chrY 59373566 2315750 0.0390030472483327 1.789181252577797