BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081241.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,318,062 number of mapped reads = 2,047,604 (88.33%) number of supplementary alignments = 22,163 (0.96%) number of secondary alignments = 0 number of mapped bases = 130,850,474 bp number of sequenced bases = 130,801,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,810 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2062 >>>>>>> ACTG content number of A's = 38,003,226 bp (29.05%) number of C's = 24,783,104 bp (18.95%) number of T's = 40,366,298 bp (30.86%) number of G's = 27,633,008 bp (21.13%) number of N's = 15,946 bp (0.01%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,203,035 number of insertions = 10,025 mapped reads with insertion percentage = 0.49% number of deletions = 30,215 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.3673X There is a 3.59% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% 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 13999262 0.056165404699232424 0.7416591730731497 chr2 243199373 7128599 0.029311749089089963 0.35591616937864884 chr3 198022430 7708784 0.03892884255586602 0.2284170323442321 chr4 191154276 6309072 0.0330051314154228 0.21807082940515538 chr5 180915260 8739637 0.04830790393248198 0.25305314927408307 chr6 171115067 9664575 0.05647997671648634 0.31579435390144894 chr7 159138663 8865712 0.055710610060862455 0.5089159644508281 chr8 146364022 6677626 0.045623411469247546 0.41356015136096713 chr9 141213431 5123810 0.03628415486909315 0.2992301665070435 chr10 135534747 4015097 0.029624115504491257 0.3543033665804429 chr11 135006516 6239711 0.0462178506998877 0.3181462242946235 chr12 133851895 3999505 0.02988007752897335 0.20220557192555755 chr13 115169878 3747393 0.03253796101095115 0.20557233052326127 chr14 107349540 5232104 0.04873895128008932 0.26479633580652334 chr15 102531392 4327421 0.042205815366283136 0.2399427931852089 chr16 90354753 3499079 0.03872600924491487 0.2474627504306024 chr17 81195210 1958879 0.024125548785451752 0.1889423689212956 chr18 78077248 4129666 0.05289205377730526 0.5013362172824546 chr19 59128983 3309724 0.05597464783048949 0.5146223190356817 chr20 63025520 2766822 0.043900026528936216 0.2419661127892016 chr21 48129895 2006286 0.0416848197985888 0.24398387810527514 chr22 51304566 967716 0.018862180804726035 0.15354289383672579 chrMT 16571 12278 0.7409329551626335 0.9528840948079476 chrX 155270560 10057240 0.06477235607316674 0.3161106027046513 chrY 59373566 364476 0.006138691416985128 0.12131378556533182