BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504666.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 89,173,462 number of mapped reads = 88,782,516 (99.56%) number of supplementary alignments = 1,138,772 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 44,480,764 number of mapped paired reads (second in pair) = 44,301,752 number of mapped paired reads (both in pair) = 88,566,880 number of mapped paired reads (singletons) = 215,636 number of mapped bases = 8,269,648,992 bp number of sequenced bases = 8,262,806,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,505,880 duplication rate = 27.19% >>>>>>> Insert size mean insert size = 38,638.9844 std insert size = 1,842,593.6049 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 51.1836 >>>>>>> ACTG content number of A's = 2,496,646,180 bp (30.22%) number of C's = 1,632,301,881 bp (19.75%) number of T's = 2,518,046,398 bp (30.47%) number of G's = 1,611,123,823 bp (19.5%) number of N's = 4,687,774 bp (0.06%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 83,117,687 number of insertions = 2,641,979 mapped reads with insertion percentage = 2.91% number of deletions = 2,825,340 mapped reads with deletion percentage = 3.1% homopolymer indels = 37.98% >>>>>>> Coverage mean coverageData = 2.6713X std coverageData = 339.4808X There is a 26.7% of reference with a coverageData >= 1X There is a 19.08% of reference with a coverageData >= 2X There is a 13.35% of reference with a coverageData >= 3X There is a 10.58% of reference with a coverageData >= 4X There is a 8.61% of reference with a coverageData >= 5X There is a 7.27% of reference with a coverageData >= 6X There is a 6.25% of reference with a coverageData >= 7X There is a 5.47% of reference with a coverageData >= 8X There is a 4.84% of reference with a coverageData >= 9X There is a 4.34% of reference with a coverageData >= 10X There is a 3.92% of reference with a coverageData >= 11X There is a 3.56% of reference with a coverageData >= 12X There is a 3.26% of reference with a coverageData >= 13X There is a 3% of reference with a coverageData >= 14X There is a 2.78% of reference with a coverageData >= 15X There is a 2.58% of reference with a coverageData >= 16X There is a 2.4% of reference with a coverageData >= 17X There is a 2.24% of reference with a coverageData >= 18X There is a 2.1% of reference with a coverageData >= 19X There is a 1.98% of reference with a coverageData >= 20X There is a 1.86% of reference with a coverageData >= 21X There is a 1.76% of reference with a coverageData >= 22X There is a 1.66% of reference with a coverageData >= 23X There is a 1.58% of reference with a coverageData >= 24X There is a 1.5% of reference with a coverageData >= 25X There is a 1.42% of reference with a coverageData >= 26X There is a 1.36% of reference with a coverageData >= 27X There is a 1.3% of reference with a coverageData >= 28X There is a 1.24% of reference with a coverageData >= 29X There is a 1.18% of reference with a coverageData >= 30X There is a 1.13% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 1.04% of reference with a coverageData >= 33X There is a 1% of reference with a coverageData >= 34X There is a 0.96% of reference with a coverageData >= 35X There is a 0.93% of reference with a coverageData >= 36X There is a 0.89% of reference with a coverageData >= 37X There is a 0.86% of reference with a coverageData >= 38X There is a 0.83% of reference with a coverageData >= 39X There is a 0.8% of reference with a coverageData >= 40X There is a 0.78% of reference with a coverageData >= 41X There is a 0.75% of reference with a coverageData >= 42X There is a 0.73% of reference with a coverageData >= 43X There is a 0.71% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.66% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.62% of reference with a coverageData >= 48X There is a 0.61% of reference with a coverageData >= 49X There is a 0.59% of reference with a coverageData >= 50X There is a 0.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 539506320 2.164513443679645 23.758287296134558 chr2 243199373 2413298801 9.923129205600379 1209.8365513885965 chr3 198022430 533382611 2.693546438148446 15.407434455161727 chr4 191154276 500197788 2.6167229866205033 17.711761162489314 chr5 180915260 422321268 2.334359567014966 15.17204573665779 chr6 171115067 392263865 2.292398161524841 11.634028010911925 chr7 159138663 332615556 2.0900989723660053 11.430265335920973 chr8 146364022 393872556 2.6910476401092613 25.703636729392084 chr9 141213431 320327288 2.268391085264404 25.746897845577738 chr10 135534747 305732153 2.255747398857062 13.804446455426048 chr11 135006516 300858062 2.2284706761857334 13.637279616841147 chr12 133851895 310477111 2.319557082101826 11.453219582246255 chr13 115169878 198847566 1.7265587969104212 9.016461484783816 chr14 107349540 215046439 2.003235775393169 11.971650021145543 chr15 102531392 190720041 1.8601136420736393 29.39023618038305 chr16 90354753 145357593 1.6087431836596355 10.226335880120441 chr17 81195210 121458358 1.4958808284380323 6.900921542737725 chr18 78077248 209745216 2.6863807494854326 15.107598551307335 chr19 59128983 87364782 1.477528913358784 18.313760077439433 chr20 63025520 117322191 1.8615029435695254 10.379772724067717 chr21 48129895 89305609 1.8555122341322374 12.860081054978515 chr22 51304566 61314818 1.1951142516243096 11.466375312679638 chrMT 16571 1529 0.09226962766278438 0.445030339251833 chrX 155270560 15452146 0.09951755181407215 3.3056919078854974 chrY 59373566 52859325 0.8902838175493788 7.850628947399014