BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472791.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 = 10,039,032 number of mapped reads = 9,949,434 (99.11%) number of supplementary alignments = 35,207 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,989,864 number of mapped paired reads (second in pair) = 4,959,570 number of mapped paired reads (both in pair) = 9,897,024 number of mapped paired reads (singletons) = 52,410 number of mapped bases = 977,248,467 bp number of sequenced bases = 977,114,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,664,669 duplication rate = 45.15% >>>>>>> Insert size mean insert size = 22,120.0227 std insert size = 1,479,438.6325 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.1182 >>>>>>> ACTG content number of A's = 270,214,895 bp (27.65%) number of C's = 219,811,889 bp (22.5%) number of T's = 268,033,734 bp (27.43%) number of G's = 218,862,609 bp (22.4%) number of N's = 190,926 bp (0.02%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 5,824,312 number of insertions = 58,612 mapped reads with insertion percentage = 0.58% number of deletions = 53,005 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.3157X std coverageData = 11.4094X There is a 3.04% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 112261346 0.45039545157241556 13.877054017383838 chr2 243199373 80364560 0.33044723351322125 19.4757350538254 chr3 198022430 111884109 0.5650072519562557 13.506327330029363 chr4 191154276 36378620 0.19031026017958394 7.402950340823806 chr5 180915260 49192515 0.2719091523843815 10.02037738187611 chr6 171115067 54498944 0.31849295889297696 8.640366008725513 chr7 159138663 36551536 0.2296835684738661 9.304925848712124 chr8 146364022 54940755 0.3753706289924173 12.946646428748055 chr9 141213431 64324330 0.45551141661588834 12.93267737446019 chr10 135534747 26817145 0.19786177045802136 6.811041727246795 chr11 135006516 38410732 0.28451020838134955 9.766510281242708 chr12 133851895 53642124 0.4007572997005384 12.265559759184265 chr13 115169878 25291167 0.21959879995705128 8.387629083244269 chr14 107349540 17853381 0.16631073593794626 5.555393790996081 chr15 102531392 21053834 0.205340370293617 8.165208766571693 chr16 90354753 37228848 0.4120297689264891 13.38548311623695 chr17 81195210 34773186 0.4282664703989312 10.370223981614522 chr18 78077248 12813497 0.16411307171072423 6.200250275380736 chr19 59128983 15757539 0.26649433493554253 8.259334238936665 chr20 63025520 26905932 0.42690535516406686 14.189665470737209 chr21 48129895 3463629 0.07196419190193537 3.7706631854231385 chr22 51304566 8509984 0.1658718641143948 5.21046472180556 chrMT 16571 1779 0.1073562247299499 0.389440922363118 chrX 155270560 51172356 0.32956895370249195 10.923179128004234 chrY 59373566 3156619 0.05316539350188264 2.6585612718248197