BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514736.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 145,705,723 number of mapped reads = 142,113,014 (97.53%) number of supplementary alignments = 3,750,692 (2.57%) number of secondary alignments = 0 number of mapped bases = 13,632,448,016 bp number of sequenced bases = 13,625,261,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,012,073 duplication rate = 51.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.1997 >>>>>>> ACTG content number of A's = 3,582,731,567 bp (26.29%) number of C's = 3,176,244,402 bp (23.31%) number of T's = 3,614,903,665 bp (26.53%) number of G's = 3,181,824,274 bp (23.35%) number of N's = 69,557,974 bp (0.51%) GC percentage = 46.66% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 127,336,299 number of insertions = 4,330,949 mapped reads with insertion percentage = 2.94% number of deletions = 3,513,930 mapped reads with deletion percentage = 2.41% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 4.4037X std coverageData = 81.9485X There is a 8.08% of reference with a coverageData >= 1X There is a 5.34% of reference with a coverageData >= 2X There is a 4.23% of reference with a coverageData >= 3X There is a 3.69% of reference with a coverageData >= 4X There is a 3.35% of reference with a coverageData >= 5X There is a 3.1% of reference with a coverageData >= 6X There is a 2.92% of reference with a coverageData >= 7X There is a 2.77% of reference with a coverageData >= 8X There is a 2.65% of reference with a coverageData >= 9X There is a 2.54% of reference with a coverageData >= 10X There is a 2.45% of reference with a coverageData >= 11X There is a 2.37% of reference with a coverageData >= 12X There is a 2.3% of reference with a coverageData >= 13X There is a 2.23% of reference with a coverageData >= 14X There is a 2.17% of reference with a coverageData >= 15X There is a 2.12% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 2.02% of reference with a coverageData >= 18X There is a 1.98% of reference with a coverageData >= 19X There is a 1.94% of reference with a coverageData >= 20X There is a 1.9% of reference with a coverageData >= 21X There is a 1.87% of reference with a coverageData >= 22X There is a 1.83% of reference with a coverageData >= 23X There is a 1.8% of reference with a coverageData >= 24X There is a 1.77% of reference with a coverageData >= 25X There is a 1.74% of reference with a coverageData >= 26X There is a 1.71% of reference with a coverageData >= 27X There is a 1.68% of reference with a coverageData >= 28X There is a 1.66% of reference with a coverageData >= 29X There is a 1.63% of reference with a coverageData >= 30X There is a 1.61% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.56% of reference with a coverageData >= 33X There is a 1.54% of reference with a coverageData >= 34X There is a 1.52% of reference with a coverageData >= 35X There is a 1.5% of reference with a coverageData >= 36X There is a 1.48% of reference with a coverageData >= 37X There is a 1.46% of reference with a coverageData >= 38X There is a 1.44% of reference with a coverageData >= 39X There is a 1.42% of reference with a coverageData >= 40X There is a 1.41% of reference with a coverageData >= 41X There is a 1.39% of reference with a coverageData >= 42X There is a 1.37% of reference with a coverageData >= 43X There is a 1.36% of reference with a coverageData >= 44X There is a 1.34% of reference with a coverageData >= 45X There is a 1.33% of reference with a coverageData >= 46X There is a 1.31% of reference with a coverageData >= 47X There is a 1.3% of reference with a coverageData >= 48X There is a 1.28% of reference with a coverageData >= 49X There is a 1.27% of reference with a coverageData >= 50X There is a 1.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 504930525 2.0257944512804245 39.07051042336819 chr2 243199373 963812558 3.9630552748176697 102.1495056610097 chr3 198022430 620218211 3.1320603984104225 64.37423563972258 chr4 191154276 489217482 2.5592808711221298 44.16626148747235 chr5 180915260 428426909 2.368108190541804 29.55665975657709 chr6 171115067 812885123 4.75051751579538 61.33296700814422 chr7 159138663 229570272 1.4425801227197692 22.493091183705875 chr8 146364022 1374263930 9.389356149286469 117.54461287099149 chr9 141213431 684143213 4.8447460567684955 126.98795116882401 chr10 135534747 800273087 5.90456030437715 85.88693170479888 chr11 135006516 365653488 2.708413629457707 35.483013463256476 chr12 133851895 378329197 2.8264762108896555 32.62476867883724 chr13 115169878 158932469 1.3799829587385688 55.368935449770454 chr14 107349540 328975616 3.064527486563985 49.949231624880454 chr15 102531392 273824818 2.670643718559873 37.90750065738977 chr16 90354753 530458343 5.870840496902249 102.90540583162336 chr17 81195210 725090203 8.930209097310051 75.84254887050255 chr18 78077248 186292446 2.3860016941170876 35.01400888651324 chr19 59128983 3042284219 51.4516581318505 346.68160995383346 chr20 63025520 314179354 4.98495457078339 47.41611748657615 chr21 48129895 34651965 0.7199676001786416 23.283150423486262 chr22 51304566 87473375 1.7049822622025494 26.074738703778635 chrMT 16571 14480062 873.8194436063002 356.00436621001916 chrX 155270560 247312252 1.5927826369660805 27.961120383022482 chrY 59373566 36768899 0.6192806239733015 71.51971454462097