BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927040.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 = 20,499,194 number of mapped reads = 19,770,824 (96.45%) number of supplementary alignments = 791,361 (3.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,936,504 number of mapped paired reads (second in pair) = 9,834,320 number of mapped paired reads (both in pair) = 19,335,332 number of mapped paired reads (singletons) = 435,492 number of mapped bases = 1,779,505,003 bp number of sequenced bases = 1,778,196,534 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,603,120 duplication rate = 6.4% >>>>>>> Insert size mean insert size = 415,124.0434 std insert size = 6,299,466.0298 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.3569 >>>>>>> ACTG content number of A's = 511,449,489 bp (28.76%) number of C's = 341,825,681 bp (19.22%) number of T's = 525,024,007 bp (29.53%) number of G's = 399,679,036 bp (22.48%) number of N's = 218,321 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 18,787,619 number of insertions = 308,460 mapped reads with insertion percentage = 1.53% number of deletions = 881,111 mapped reads with deletion percentage = 4.34% homopolymer indels = 51.25% >>>>>>> Coverage mean coverageData = 0.5748X std coverageData = 2.3285X There is a 28.98% of reference with a coverageData >= 1X There is a 13.37% of reference with a coverageData >= 2X There is a 6.32% of reference with a coverageData >= 3X There is a 3.3% of reference with a coverageData >= 4X There is a 1.81% of reference with a coverageData >= 5X There is a 1.04% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% 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% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 146520376 0.5878435745201213 3.2562208397929084 chr2 243199373 158647865 0.6523366530225388 3.920358358865221 chr3 198022430 118567934 0.5987601202550641 1.254299505590699 chr4 191154276 113936567 0.5960450866398616 1.9997288836763625 chr5 180915260 110498786 0.6107764817627878 1.2559752244441202 chr6 171115067 99145501 0.5794083638467675 1.2971641472712738 chr7 159138663 95440517 0.5997318011902614 1.8539209048530396 chr8 146364022 92771466 0.6338406442534081 1.5242859320625919 chr9 141213431 77781916 0.5508110343979957 2.8391207704303594 chr10 135534747 86596840 0.6389272265362328 4.246593350621794 chr11 135006516 86109327 0.6378160814104706 2.0847888187029504 chr12 133851895 83422624 0.6232457448585245 1.3084200947400735 chr13 115169878 56396485 0.4896808608236956 1.1253307022417485 chr14 107349540 53508368 0.4984499048621913 1.2304831255073094 chr15 102531392 47578525 0.4640386136569764 1.108598253312434 chr16 90354753 49937229 0.5526796028096054 3.175719833981297 chr17 81195210 39511091 0.4866184963374071 1.545856493494167 chr18 78077248 45018048 0.5765834369572043 2.7147928694808896 chr19 59128983 26691287 0.45140784849960974 1.787356316010966 chr20 63025520 40615271 0.6444257976768776 1.395964982467454 chr21 48129895 22988781 0.4776403729947884 1.6182658320312 chr22 51304566 19791860 0.38577190186152244 1.0949294537472698 chrMT 16571 106143 6.405346690000603 3.349255196037192 chrX 155270560 103375253 0.6657749736975251 1.51115534470936 chrY 59373566 4546943 0.07658194220640209 2.822398135178329