BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618581.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 57,109,194 number of mapped reads = 53,649,451 (93.94%) number of supplementary alignments = 81,975 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,157,674 number of mapped paired reads (second in pair) = 26,491,777 number of mapped paired reads (both in pair) = 52,515,410 number of mapped paired reads (singletons) = 1,134,041 number of mapped bases = 5,111,164,101 bp number of sequenced bases = 5,107,858,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,497,489 duplication rate = 18.79% >>>>>>> Insert size mean insert size = 29,669.7089 std insert size = 1,691,205.8802 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.9952 >>>>>>> ACTG content number of A's = 1,373,356,499 bp (26.89%) number of C's = 1,149,314,206 bp (22.5%) number of T's = 1,379,750,866 bp (27.01%) number of G's = 1,205,205,476 bp (23.6%) number of N's = 231,596 bp (0%) GC percentage = 46.1% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 64,553,130 number of insertions = 917,819 mapped reads with insertion percentage = 1.68% number of deletions = 2,368,386 mapped reads with deletion percentage = 4.31% homopolymer indels = 52.08% >>>>>>> Coverage mean coverageData = 1.6511X std coverageData = 7.1707X There is a 27.83% of reference with a coverageData >= 1X There is a 19.17% of reference with a coverageData >= 2X There is a 14.43% of reference with a coverageData >= 3X There is a 11.45% of reference with a coverageData >= 4X There is a 9.35% of reference with a coverageData >= 5X There is a 7.82% of reference with a coverageData >= 6X There is a 6.65% of reference with a coverageData >= 7X There is a 5.74% of reference with a coverageData >= 8X There is a 5% of reference with a coverageData >= 9X There is a 4.39% of reference with a coverageData >= 10X There is a 3.89% of reference with a coverageData >= 11X There is a 3.47% of reference with a coverageData >= 12X There is a 3.11% of reference with a coverageData >= 13X There is a 2.8% of reference with a coverageData >= 14X There is a 2.53% of reference with a coverageData >= 15X There is a 2.3% of reference with a coverageData >= 16X There is a 2.1% of reference with a coverageData >= 17X There is a 1.92% of reference with a coverageData >= 18X There is a 1.76% of reference with a coverageData >= 19X There is a 1.62% of reference with a coverageData >= 20X There is a 1.49% of reference with a coverageData >= 21X There is a 1.38% of reference with a coverageData >= 22X There is a 1.28% of reference with a coverageData >= 23X There is a 1.19% of reference with a coverageData >= 24X There is a 1.1% of reference with a coverageData >= 25X There is a 1.03% of reference with a coverageData >= 26X There is a 0.96% of reference with a coverageData >= 27X There is a 0.89% of reference with a coverageData >= 28X There is a 0.84% of reference with a coverageData >= 29X There is a 0.78% of reference with a coverageData >= 30X There is a 0.74% of reference with a coverageData >= 31X There is a 0.69% of reference with a coverageData >= 32X There is a 0.65% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.58% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.51% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.46% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.34% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 468323727 1.87892702181071 7.931604479507017 chr2 243199373 421364126 1.7325872217606417 8.730188600624972 chr3 198022430 316721005 1.59941984854948 5.594579657503931 chr4 191154276 227310729 1.1891480209419956 5.196597006078361 chr5 180915260 276990290 1.5310498959568142 5.470707021070984 chr6 171115067 262381889 1.533365200388812 5.518916104755389 chr7 159138663 247804932 1.557163591351776 5.6325715644033645 chr8 146364022 238255633 1.6278292284151634 6.4196104214536485 chr9 141213431 220890682 1.564232810121298 6.510879806222853 chr10 135534747 256183957 1.8901718022168883 6.545848996156278 chr11 135006516 264309056 1.9577503651749668 7.009794119679491 chr12 133851895 227132547 1.6968945191250375 6.328866889138344 chr13 115169878 126187508 1.095664163159051 4.470515601611515 chr14 107349540 156952888 1.462073223602076 5.763422425478615 chr15 102531392 168007859 1.6385992204221709 6.364838801700393 chr16 90354753 202142749 2.237212125409717 17.49022639441445 chr17 81195210 180870529 2.2276009754762627 7.630937110571253 chr18 78077248 127914814 1.638310996822019 6.266243218945341 chr19 59128983 128431091 2.1720497205236895 8.126540957233104 chr20 63025520 157048394 2.4918222650126487 8.02413246277115 chr21 48129895 66594764 1.3836465672738325 9.03833369177941 chr22 51304566 110667991 2.1570787871005477 8.313209611791907 chrMT 16571 4719 0.28477460623981654 0.9166681372309451 chrX 155270560 250480677 1.6131884692114205 5.536442730019079 chrY 59373566 8191545 0.1379661952593516 5.881550825575564