BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472611.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,197,354 number of mapped reads = 18,062,336 (99.26%) number of supplementary alignments = 85,397 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,049,743 number of mapped paired reads (second in pair) = 9,012,593 number of mapped paired reads (both in pair) = 17,974,808 number of mapped paired reads (singletons) = 87,528 number of mapped bases = 1,777,580,939 bp number of sequenced bases = 1,777,327,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,406,334 duplication rate = 49.86% >>>>>>> Insert size mean insert size = 17,516.8872 std insert size = 1,273,590.1167 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 54.6831 >>>>>>> ACTG content number of A's = 467,029,495 bp (26.28%) number of C's = 423,799,567 bp (23.84%) number of T's = 467,176,812 bp (26.29%) number of G's = 418,987,200 bp (23.57%) number of N's = 334,320 bp (0.02%) GC percentage = 47.42% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,775,207 number of insertions = 110,503 mapped reads with insertion percentage = 0.6% number of deletions = 94,342 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.5742X std coverageData = 22.8474X There is a 3.7% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 223285377 0.895826763055487 27.94477052564493 chr2 243199373 108361609 0.4455669752076211 20.121945111128227 chr3 198022430 113173365 0.5715179083500793 20.61445078442651 chr4 191154276 41257891 0.21583556414924246 19.185607634664006 chr5 180915260 75725830 0.4185707164779798 17.236382880345506 chr6 171115067 127819445 0.7469794872008553 27.396954147663642 chr7 159138663 99804165 0.6271522150465723 21.868628943365703 chr8 146364022 136366364 0.9316931998493455 26.752794032842402 chr9 141213431 92321663 0.6537739529889335 18.67907417701976 chr10 135534747 46140784 0.3404350915267507 22.814861247962437 chr11 135006516 39697429 0.2940408372585513 10.675671962611181 chr12 133851895 93154602 0.6959528066449863 25.81665756160394 chr13 115169878 46583691 0.40447807889489995 16.824912280111526 chr14 107349540 21186516 0.1973601004717859 11.009373924499558 chr15 102531392 30403691 0.296530559148168 10.425115888301864 chr16 90354753 112571432 1.2458827926849625 38.34687709091064 chr17 81195210 62977409 0.7756296091850738 19.601392512988514 chr18 78077248 25994086 0.3329277947911279 16.98982643427523 chr19 59128983 36489179 0.6171115610089218 15.452934689614922 chr20 63025520 114508723 1.8168628041466377 55.71552140904897 chr21 48129895 10899531 0.22646072674789755 12.346938755102062 chr22 51304566 15983619 0.3115437912485216 11.24409935388869 chrMT 16571 1596 0.09631283567678474 0.3730629341341826 chrX 155270560 96527613 0.6216736321425002 25.842537153100302 chrY 59373566 6345329 0.10687128005752594 12.93849056430392