BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 14,239,022 number of mapped reads = 13,891,110 (97.56%) number of supplementary alignments = 1,388,291 (9.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,941,667 number of mapped paired reads (second in pair) = 6,949,443 number of mapped paired reads (both in pair) = 13,658,146 number of mapped paired reads (singletons) = 232,964 number of mapped bases = 1,650,990,321 bp number of sequenced bases = 1,650,058,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,381,774 duplication rate = 67.02% >>>>>>> Insert size mean insert size = 834,500.2939 std insert size = 8,423,662.0123 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.834 >>>>>>> ACTG content number of A's = 492,387,464 bp (29.84%) number of C's = 327,632,738 bp (19.86%) number of T's = 491,364,983 bp (29.78%) number of G's = 338,652,687 bp (20.52%) number of N's = 20,306 bp (0%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 16,531,426 number of insertions = 163,373 mapped reads with insertion percentage = 1.14% number of deletions = 380,621 mapped reads with deletion percentage = 2.68% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.5333X std coverageData = 7.0383X There is a 9.04% of reference with a coverageData >= 1X There is a 7.47% of reference with a coverageData >= 2X There is a 6.12% of reference with a coverageData >= 3X There is a 5.27% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 3.63% of reference with a coverageData >= 6X There is a 2.89% of reference with a coverageData >= 7X There is a 2.41% of reference with a coverageData >= 8X There is a 1.89% of reference with a coverageData >= 9X There is a 1.59% of reference with a coverageData >= 10X There is a 1.25% of reference with a coverageData >= 11X There is a 1.07% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.73% of reference with a coverageData >= 14X There is a 0.58% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.41% of reference with a coverageData >= 17X There is a 0.36% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 132344431 0.5309693130112603 4.064394117784051 chr2 243199373 140716200 0.5786042877668109 22.728524247062165 chr3 198022430 131621179 0.6646781326741622 2.637362107568575 chr4 191154276 67129029 0.35117722922400124 2.3188166417980276 chr5 180915260 99702910 0.5511028201822223 2.3211616958028047 chr6 171115067 96037641 0.561245965558369 2.7483298741168007 chr7 159138663 83567182 0.5251218052523163 3.4000865250907006 chr8 146364022 90873175 0.6208709883635201 3.4379215190783614 chr9 141213431 69487647 0.49207533949090154 2.9234795135681493 chr10 135534747 80992463 0.5975771143026518 5.087799821667805 chr11 135006516 60322768 0.4468137523080738 2.1541250975951383 chr12 133851895 81729154 0.6105939254726278 2.4965379673960304 chr13 115169878 37784382 0.3280752107769012 1.7928856235454764 chr14 107349540 52982727 0.49355336781135717 2.224535721721085 chr15 102531392 61112477 0.596036743556549 2.4703563572554503 chr16 90354753 55038438 0.6091371640405016 3.0702380792384667 chr17 81195210 81119698 0.999069994399916 3.9306067971541547 chr18 78077248 28969728 0.3710393071231199 4.675625320501672 chr19 59128983 26335782 0.4453954839710333 3.0081947215630325 chr20 63025520 77811741 1.2346068862264048 4.485118893693995 chr21 48129895 19985502 0.4152409225077262 2.145439893950518 chr22 51304566 14277590 0.27829082503105085 1.5881775128639892 chrMT 16571 3156080 190.45802908695916 145.86646196882657 chrX 155270560 55640643 0.3583463793780354 1.8770251947660692 chrY 59373566 2251754 0.03792519384805016 1.2902550803610822