BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472680.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 = 18,325,896 number of mapped reads = 18,164,847 (99.12%) number of supplementary alignments = 110,584 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,106,282 number of mapped paired reads (second in pair) = 9,058,565 number of mapped paired reads (both in pair) = 18,054,940 number of mapped paired reads (singletons) = 109,907 number of mapped bases = 1,786,484,250 bp number of sequenced bases = 1,786,149,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,538,105 duplication rate = 49.56% >>>>>>> Insert size mean insert size = 26,113.2457 std insert size = 1,626,441.7669 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 54.8754 >>>>>>> ACTG content number of A's = 483,159,543 bp (27.05%) number of C's = 412,864,170 bp (23.11%) number of T's = 482,110,135 bp (26.99%) number of G's = 407,681,851 bp (22.82%) number of N's = 333,360 bp (0.02%) GC percentage = 45.94% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 11,841,769 number of insertions = 119,961 mapped reads with insertion percentage = 0.65% number of deletions = 105,192 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.5771X std coverageData = 25.7221X There is a 3.76% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% 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 0.28% 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 0.26% 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 220377015 0.8841583387669875 39.90747669493522 chr2 243199373 110689151 0.4551374850789603 18.013986178529162 chr3 198022430 171237631 0.8647385601721986 25.28530373156787 chr4 191154276 52671032 0.2755420025236579 18.611114818315475 chr5 180915260 77579146 0.42881482745015537 17.71593318312569 chr6 171115067 120045083 0.7015459544541451 22.030660726563617 chr7 159138663 88454927 0.5558355545565945 20.62432568616604 chr8 146364022 109133124 0.7456280751836677 28.312863555851415 chr9 141213431 106391544 0.7534095251888611 20.429144507099814 chr10 135534747 37059599 0.27343245787738846 11.298560583759206 chr11 135006516 99097328 0.7340188528381845 54.414816009194055 chr12 133851895 51759577 0.3866928966526772 15.412591340118768 chr13 115169878 43355147 0.37644519342114785 14.764530479980843 chr14 107349540 20567343 0.1915922788304449 10.26003927823837 chr15 102531392 21313537 0.20787328236019656 9.345233752672764 chr16 90354753 85725403 0.9487647318343065 28.65290803363488 chr17 81195210 78243638 0.9636484467495066 48.694411448920626 chr18 78077248 9508212 0.12177954837752478 5.152867564541344 chr19 59128983 66281085 1.1209576359532516 32.51601094461274 chr20 63025520 70163311 1.113252393633563 26.218201846461543 chr21 48129895 11009055 0.22873631866431457 14.919674965882228 chr22 51304566 24074943 0.4692553680309858 17.70010385925627 chrMT 16571 3699 0.2232212902057812 0.5837187820174826 chrX 155270560 110459839 0.7114023353815431 25.356477072011934 chrY 59373566 1283881 0.021623781195827113 0.6777005211499647