BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124848.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 89,272,918 number of mapped reads = 68,446,323 (76.67%) number of supplementary alignments = 1,558,902 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 34,366,661 number of mapped paired reads (second in pair) = 34,079,662 number of mapped paired reads (both in pair) = 66,178,712 number of mapped paired reads (singletons) = 2,267,611 number of mapped bases = 8,094,230,715 bp number of sequenced bases = 8,088,314,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,227,470 duplication rate = 34.65% >>>>>>> Insert size mean insert size = 93,014.2629 std insert size = 2,932,383.4744 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.8175 >>>>>>> ACTG content number of A's = 2,383,757,996 bp (29.47%) number of C's = 1,599,679,192 bp (19.78%) number of T's = 2,374,469,839 bp (29.36%) number of G's = 1,730,288,088 bp (21.39%) number of N's = 119,209 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 94,655,678 number of insertions = 1,469,997 mapped reads with insertion percentage = 2% number of deletions = 2,665,364 mapped reads with deletion percentage = 3.73% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 2.6147X std coverageData = 38.7174X There is a 46.58% of reference with a coverageData >= 1X There is a 36.2% of reference with a coverageData >= 2X There is a 26.45% of reference with a coverageData >= 3X There is a 21.57% of reference with a coverageData >= 4X There is a 16.83% of reference with a coverageData >= 5X There is a 13.98% of reference with a coverageData >= 6X There is a 11.32% of reference with a coverageData >= 7X There is a 9.52% of reference with a coverageData >= 8X There is a 7.89% of reference with a coverageData >= 9X There is a 6.71% of reference with a coverageData >= 10X There is a 5.66% of reference with a coverageData >= 11X There is a 4.86% of reference with a coverageData >= 12X There is a 4.15% of reference with a coverageData >= 13X There is a 3.59% of reference with a coverageData >= 14X There is a 3.1% of reference with a coverageData >= 15X There is a 2.7% of reference with a coverageData >= 16X There is a 2.36% of reference with a coverageData >= 17X There is a 2.07% of reference with a coverageData >= 18X There is a 1.81% of reference with a coverageData >= 19X There is a 1.6% of reference with a coverageData >= 20X There is a 1.41% of reference with a coverageData >= 21X There is a 1.26% of reference with a coverageData >= 22X There is a 1.12% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.64% of reference with a coverageData >= 28X There is a 0.58% of reference with a coverageData >= 29X There is a 0.53% of reference with a coverageData >= 30X There is a 0.48% of reference with a coverageData >= 31X There is a 0.43% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% 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 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% 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 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 646229611 2.592690073979796 30.273393390222196 chr2 243199373 767339019 3.155185021796911 47.608132015940825 chr3 198022430 559606822 2.8259769461469593 7.4729870039029835 chr4 191154276 454777216 2.379110870635193 27.921246534882073 chr5 180915260 433004263 2.393409284545704 8.471808909905235 chr6 171115067 480127156 2.8058730561698577 15.606457069079001 chr7 159138663 476132574 2.9919352407780377 26.034047887950003 chr8 146364022 473342663 3.2340096734974937 10.782024472696204 chr9 141213431 317765830 2.2502521732511407 36.184241919735165 chr10 135534747 466380880 3.4410429083547114 137.12467143861056 chr11 135006516 339976675 2.518224194452955 14.821919762864194 chr12 133851895 373736635 2.7921654377773284 5.926993265346383 chr13 115169878 242179419 2.1028017325849735 4.694489390258056 chr14 107349540 299715100 2.791955140189702 7.836475096486342 chr15 102531392 214538181 2.0924145943517476 5.502799564293597 chr16 90354753 261244575 2.8913207808780133 51.49780541993141 chr17 81195210 174926072 2.1543890581722738 27.341465211189796 chr18 78077248 151143502 1.9358200483705574 37.88180875240046 chr19 59128983 117829188 1.9927484293108846 17.343231257731453 chr20 63025520 162455074 2.577607832509752 21.61147130175616 chr21 48129895 85890160 1.7845490832672708 16.14884756099196 chr22 51304566 64695313 1.2610049756585018 5.891633557607783 chrMT 16571 3585030 216.34361233480178 114.01112997581839 chrX 155270560 373012417 2.402338324792543 9.462329589518976 chrY 59373566 154597340 2.6038075597480534 65.14174112104632