BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472523.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 = 14,473,544 number of mapped reads = 14,352,221 (99.16%) number of supplementary alignments = 51,805 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,197,869 number of mapped paired reads (second in pair) = 7,154,352 number of mapped paired reads (both in pair) = 14,279,836 number of mapped paired reads (singletons) = 72,385 number of mapped bases = 1,415,145,271 bp number of sequenced bases = 1,414,953,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,946,440 duplication rate = 45.12% >>>>>>> Insert size mean insert size = 25,112.4867 std insert size = 1,554,560.9119 median insert size = 245 >>>>>>> Mapping quality mean mapping quality = 55.0545 >>>>>>> ACTG content number of A's = 398,207,621 bp (28.14%) number of C's = 311,245,022 bp (22%) number of T's = 395,785,653 bp (27.97%) number of G's = 309,495,505 bp (21.87%) number of N's = 219,505 bp (0.02%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,558,184 number of insertions = 78,808 mapped reads with insertion percentage = 0.54% number of deletions = 74,691 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.4571X std coverageData = 18.5238X There is a 4.54% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171849737 0.6894656322641619 32.403366923143224 chr2 243199373 122767635 0.5048024322003495 19.706792319847537 chr3 198022430 166158208 0.8390878144460706 18.99241132282319 chr4 191154276 48423512 0.25332162593108826 10.930840306358647 chr5 180915260 88140147 0.4871902292819301 20.206073514278923 chr6 171115067 92259831 0.5391683655770652 16.005661516869257 chr7 159138663 51435757 0.32321345441993565 10.415134038052328 chr8 146364022 67270173 0.4596086666708298 16.110538188857372 chr9 141213431 61498538 0.43550062883182833 11.608640711643105 chr10 135534747 27985094 0.2064791104822736 7.489377053478991 chr11 135006516 64824892 0.4801612094041446 21.208576560261996 chr12 133851895 69434690 0.5187426745060277 14.900563482031329 chr13 115169878 28468132 0.24718383395352733 9.215501023487777 chr14 107349540 30171791 0.2810612043610061 9.717191536183435 chr15 102531392 37792631 0.3685957077418787 10.662877059696518 chr16 90354753 34809216 0.3852505246735609 12.765252528467977 chr17 81195210 43450002 0.5351301142025496 12.8439426761077 chr18 78077248 40208536 0.5149840322240866 42.28996567034635 chr19 59128983 28570811 0.48319469658390707 14.672694403510171 chr20 63025520 26322066 0.4176413935180543 16.295760979415867 chr21 48129895 5193141 0.10789844856299811 5.049179165389155 chr22 51304566 12875226 0.25095672771113586 8.188270066969036 chrMT 16571 4091 0.24687707440709675 0.6456575397332072 chrX 155270560 93183119 0.6001338502289165 23.823489223118784 chrY 59373566 2048295 0.03449843319163279 1.2237391287953172