BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819137.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,727,584 number of mapped reads = 1,593,533 (92.24%) number of supplementary alignments = 7,684 (0.44%) number of secondary alignments = 0 number of mapped bases = 93,339,847 bp number of sequenced bases = 93,311,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,244 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9618 >>>>>>> ACTG content number of A's = 23,108,055 bp (24.76%) number of C's = 17,567,414 bp (18.83%) number of T's = 29,920,021 bp (32.06%) number of G's = 22,715,039 bp (24.34%) number of N's = 1,363 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 466,608 number of insertions = 6,298 mapped reads with insertion percentage = 0.39% number of deletions = 16,630 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.2858X There is a 2.49% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% 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 9251999 0.03711926158049572 0.4889454481350099 chr2 243199373 7207215 0.029635006501435347 0.34770157408563135 chr3 198022430 4965054 0.025073189941159695 0.18596096087344227 chr4 191154276 5216066 0.02728720544028008 0.24076789131083273 chr5 180915260 4977025 0.027510255353804868 0.19467269549514266 chr6 171115067 4080265 0.02384515327338182 0.21634869866845138 chr7 159138663 4698987 0.029527626482572622 0.34233824297000864 chr8 146364022 8587905 0.05867497273339482 0.35537284475836134 chr9 141213431 4053808 0.02870695776806103 0.23429046313456492 chr10 135534747 4894642 0.036113558392520555 0.3315365907871218 chr11 135006516 3290834 0.024375371630210797 0.24225898901570733 chr12 133851895 4328567 0.0323384812743966 0.2116373170677505 chr13 115169878 2089147 0.0181396996877951 0.15690339141455373 chr14 107349540 2145432 0.01998547921118246 0.16962198285118585 chr15 102531392 2366477 0.023080511771458246 0.1785650815461217 chr16 90354753 2917581 0.032290288038306074 0.22259760828939992 chr17 81195210 3297557 0.040612703631162476 0.24863746870341696 chr18 78077248 2142559 0.027441528164517275 0.39455016176025265 chr19 59128983 1940118 0.03281162471541241 0.3555592141470835 chr20 63025520 2640696 0.04189883716945136 0.24899330649015133 chr21 48129895 1325775 0.027545769630289034 0.22639759685514207 chr22 51304566 765053 0.014911986586145178 0.14310906453804298 chrMT 16571 31307 1.889264377527005 1.8417796790367236 chrX 155270560 5766134 0.03713604175833461 0.2403492512896392 chrY 59373566 359644 0.00605730839882516 0.19632397041069405