BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,499,884 number of mapped reads = 21,074,927 (98.02%) number of supplementary alignments = 581,620 (2.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,582,129 number of mapped paired reads (second in pair) = 10,492,798 number of mapped paired reads (both in pair) = 20,814,386 number of mapped paired reads (singletons) = 260,541 number of mapped bases = 1,961,604,075 bp number of sequenced bases = 1,960,144,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,493,628 duplication rate = 5.59% >>>>>>> Insert size mean insert size = 279,197.9148 std insert size = 5,200,780.2095 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.6318 >>>>>>> ACTG content number of A's = 559,684,812 bp (28.55%) number of C's = 390,434,118 bp (19.92%) number of T's = 568,065,333 bp (28.98%) number of G's = 441,810,170 bp (22.54%) number of N's = 149,903 bp (0.01%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 18,230,167 number of insertions = 331,167 mapped reads with insertion percentage = 1.55% number of deletions = 1,000,842 mapped reads with deletion percentage = 4.63% homopolymer indels = 52.25% >>>>>>> Coverage mean coverageData = 0.6337X std coverageData = 2.5532X There is a 29.54% of reference with a coverageData >= 1X There is a 14.94% of reference with a coverageData >= 2X There is a 7.56% of reference with a coverageData >= 3X There is a 4.17% of reference with a coverageData >= 4X There is a 2.37% of reference with a coverageData >= 5X There is a 1.39% of reference with a coverageData >= 6X There is a 0.84% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 159640269 0.6404809278288619 2.8426212992642665 chr2 243199373 171510363 0.7052253502314745 4.56013339557013 chr3 198022430 133757307 0.6754654359104673 1.3913454234361147 chr4 191154276 119409207 0.6246745272912441 2.031683810273423 chr5 180915260 119253212 0.6591661311489146 1.3607280462610267 chr6 171115067 113360582 0.6624815919921301 2.019249519897442 chr7 159138663 100826050 0.6335735647094132 2.210699727603785 chr8 146364022 100884344 0.6892700994510795 1.6997284319207506 chr9 141213431 82786672 0.5862521108208184 3.4100219716143374 chr10 135534747 94773130 0.6992533803896059 3.441734555917792 chr11 135006516 92459475 0.6848519444794798 2.210341670821878 chr12 133851895 88022135 0.6576084335600927 1.6879018524030673 chr13 115169878 60286393 0.5234562547682824 1.28600745267834 chr14 107349540 59580414 0.5550132212955919 1.3082569760498832 chr15 102531392 58070462 0.5663676349970943 1.3805992197600159 chr16 90354753 63743335 0.7054784932011269 5.039049175194009 chr17 81195210 49652321 0.6115178592431746 1.7205751580213706 chr18 78077248 53151677 0.6807575620493181 3.632463166446465 chr19 59128983 30636245 0.5181256880403304 1.9148823907319 chr20 63025520 45221895 0.717517205728727 1.5369977432733124 chr21 48129895 25083852 0.5211698882783766 2.0032655828662587 chr22 51304566 24234867 0.47237251748704007 1.2487786620205017 chrMT 16571 216779 13.081829702492305 10.484508442776225 chrX 155270560 111550252 0.7184249995620547 1.6423867110932175 chrY 59373566 3492837 0.05882814921374269 1.780640574816268