BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046537.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 5,321,080 number of mapped reads = 5,237,727 (98.43%) number of supplementary alignments = 31,842 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,651,101 number of mapped paired reads (second in pair) = 2,586,626 number of mapped paired reads (both in pair) = 5,165,270 number of mapped paired reads (singletons) = 72,457 number of mapped bases = 505,656,269 bp number of sequenced bases = 505,428,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,619,098 duplication rate = 23.2% >>>>>>> Insert size mean insert size = 34,610.7991 std insert size = 1,861,617.0109 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 51.7796 >>>>>>> ACTG content number of A's = 147,739,430 bp (29.23%) number of C's = 105,393,940 bp (20.85%) number of T's = 147,001,451 bp (29.08%) number of G's = 105,248,372 bp (20.82%) number of N's = 44,896 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,991,295 number of insertions = 55,599 mapped reads with insertion percentage = 1.04% number of deletions = 70,097 mapped reads with deletion percentage = 1.28% homopolymer indels = 51.38% >>>>>>> Coverage mean coverageData = 0.1633X std coverageData = 48.5704X There is a 1.9% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 39052171 0.15667832980043006 17.57902986598092 chr2 243199373 33748393 0.13876842108470402 9.419260937759637 chr3 198022430 24398032 0.12320842643936851 8.910770713254276 chr4 191154276 7567977 0.03959093753152558 1.4520686049504112 chr5 180915260 76724082 0.4240885041980428 75.55636083352866 chr6 171115067 36836205 0.2152715459007476 35.27863610098299 chr7 159138663 19531330 0.12273151999523836 36.835613814440954 chr8 146364022 125461785 0.8571900613663104 185.45133598834425 chr9 141213431 6945068 0.04918135584426102 2.8864481388013363 chr10 135534747 23840200 0.17589732911811906 24.623546151526252 chr11 135006516 10081870 0.07467691411279734 3.984866222108012 chr12 133851895 6943359 0.0518734456467725 2.174185054566352 chr13 115169878 11411687 0.09908569148610195 19.152987266877588 chr14 107349540 8682213 0.08087797115851637 3.805115570469368 chr15 102531392 6597592 0.06434704407407246 2.7866683015447182 chr16 90354753 22861719 0.2530217641123982 65.2033202736976 chr17 81195210 3982835 0.049052585737508404 1.5448425073623926 chr18 78077248 3031734 0.038829929046679514 1.0211744137564698 chr19 59128983 2828529 0.04783659140560561 1.4738584425664347 chr20 63025520 4218473 0.0669327758025638 1.2294364299337368 chr21 48129895 1577429 0.0327744118286566 3.7830624617206596 chr22 51304566 2053269 0.040021174723512916 5.178179206441462 chrMT 16571 391855 23.647033975016594 9.799657917656049 chrX 155270560 26491487 0.17061500261221443 33.58472157903611 chrY 59373566 396975 0.006686056215656645 1.4054217995682883