BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472473.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,228,334 number of mapped reads = 18,898,369 (98.28%) number of supplementary alignments = 86,470 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,474,826 number of mapped paired reads (second in pair) = 9,423,543 number of mapped paired reads (both in pair) = 18,787,392 number of mapped paired reads (singletons) = 110,977 number of mapped bases = 1,852,812,967 bp number of sequenced bases = 1,852,584,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,359,910 duplication rate = 45.33% >>>>>>> Insert size mean insert size = 29,978.887 std insert size = 1,641,089.1281 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.8565 >>>>>>> ACTG content number of A's = 513,124,735 bp (27.7%) number of C's = 415,622,635 bp (22.43%) number of T's = 508,992,443 bp (27.47%) number of G's = 414,554,470 bp (22.38%) number of N's = 289,876 bp (0.02%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,654,389 number of insertions = 97,644 mapped reads with insertion percentage = 0.51% number of deletions = 92,956 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.5985X std coverageData = 23.3997X There is a 5.89% of reference with a coverageData >= 1X There is a 2.77% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 115728056 0.4643039826167574 15.909291662813558 chr2 243199373 105818486 0.435110028018041 16.745711168988795 chr3 198022430 203805619 1.0292047168596001 27.577072903603646 chr4 191154276 85510704 0.447338693066955 16.488356746740102 chr5 180915260 126944808 0.7016810411681137 26.008033861085753 chr6 171115067 111877586 0.6538149326149053 26.501867469304905 chr7 159138663 109509497 0.6881388528443273 37.43114532994344 chr8 146364022 71474278 0.48833228974809123 14.357799507353755 chr9 141213431 124193953 0.8794769174612009 27.972596988774526 chr10 135534747 50448367 0.3722172219054646 17.342659381196558 chr11 135006516 69569025 0.5153012392379639 17.382603071445214 chr12 133851895 88101608 0.6582021718855755 21.10300666464299 chr13 115169878 80499418 0.6989624318261413 34.00864300182102 chr14 107349540 50391567 0.4694157702026483 18.025540957163702 chr15 102531392 44122761 0.43033416536469143 21.25043451824525 chr16 90354753 78634991 0.870291693454134 27.720924926877377 chr17 81195210 83597450 1.029585981734637 43.142289096274204 chr18 78077248 41409339 0.5303637110775216 17.932689929761246 chr19 59128983 42604109 0.7205283574723415 23.35616110804309 chr20 63025520 35333862 0.5606278536059679 21.328873184202962 chr21 48129895 6212100 0.12906946919373083 5.678602618435186 chr22 51304566 13021642 0.25381058676142004 7.592842360961766 chrMT 16571 5344 0.32249109890773037 0.9296868490433953 chrX 155270560 106676959 0.6870391850200064 23.382774736184217 chrY 59373566 7321438 0.12331140763888092 7.464573184679827