BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927046.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 33,288,372 number of mapped reads = 32,587,138 (97.89%) number of supplementary alignments = 301,780 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,375,777 number of mapped paired reads (second in pair) = 16,211,361 number of mapped paired reads (both in pair) = 32,179,422 number of mapped paired reads (singletons) = 407,716 number of mapped bases = 3,051,270,036 bp number of sequenced bases = 3,049,005,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,612,302 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 105,524.6627 std insert size = 3,182,361.9647 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.4771 >>>>>>> ACTG content number of A's = 877,563,078 bp (28.78%) number of C's = 601,368,321 bp (19.72%) number of T's = 890,397,556 bp (29.2%) number of G's = 679,215,141 bp (22.28%) number of N's = 461,566 bp (0.02%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 32,749,316 number of insertions = 492,927 mapped reads with insertion percentage = 1.49% number of deletions = 1,602,956 mapped reads with deletion percentage = 4.79% homopolymer indels = 52.81% >>>>>>> Coverage mean coverageData = 0.9856X std coverageData = 3.7119X There is a 36.01% of reference with a coverageData >= 1X There is a 21.22% of reference with a coverageData >= 2X There is a 12.99% of reference with a coverageData >= 3X There is a 8.38% of reference with a coverageData >= 4X There is a 5.55% of reference with a coverageData >= 5X There is a 3.76% of reference with a coverageData >= 6X There is a 2.59% of reference with a coverageData >= 7X There is a 1.81% of reference with a coverageData >= 8X There is a 1.28% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% 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 249318046 1.000270510860633 4.438501514876344 chr2 243199373 268770297 1.1051438730477319 6.726424183960485 chr3 198022430 206946648 1.0450667027972538 2.0262209685956964 chr4 191154276 184019035 0.9626728674382361 2.8894085843087223 chr5 180915260 184762465 1.0212652321313305 1.9740002826974643 chr6 171115067 178948439 1.045778388410414 2.087375005027363 chr7 159138663 155412208 0.9765835974127796 2.4985121993840984 chr8 146364022 158812702 1.0850528690718817 2.470093294607087 chr9 141213431 130643022 0.9251458666137784 4.5443949553683165 chr10 135534747 153241207 1.130641480446339 7.47256373883486 chr11 135006516 144843152 1.0728604536391413 2.8838950561016583 chr12 133851895 137555942 1.027672727382754 2.0240784224697563 chr13 115169878 91588657 0.7952483634653151 1.7506836247682847 chr14 107349540 90671231 0.8446354870267725 1.8825346719596538 chr15 102531392 89174921 0.8697328619121839 1.9007632654149058 chr16 90354753 97435038 1.0783609579453999 4.913453159395845 chr17 81195210 76901316 0.9471164124090571 3.041761941760105 chr18 78077248 82678273 1.0589291389983417 4.567421105476074 chr19 59128983 46581486 0.7877944729744464 2.79491463369421 chr20 63025520 70466539 1.1180635875753187 2.295659821179379 chr21 48129895 38480868 0.7995211292274791 2.543717238022245 chr22 51304566 34652256 0.6754224565509432 1.7506178353197042 chrMT 16571 23697 1.4300283628024864 1.8051034032540663 chrX 155270560 174346405 1.1228555174915322 2.4977041386202647 chrY 59373566 4996186 0.08414832284117818 3.804552463102631