BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472788.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 = 11,040,566 number of mapped reads = 10,938,023 (99.07%) number of supplementary alignments = 45,843 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,488,585 number of mapped paired reads (second in pair) = 5,449,438 number of mapped paired reads (both in pair) = 10,874,190 number of mapped paired reads (singletons) = 63,833 number of mapped bases = 1,073,868,106 bp number of sequenced bases = 1,073,719,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,863,019 duplication rate = 44.21% >>>>>>> Insert size mean insert size = 24,661.98 std insert size = 1,530,152.1866 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.8971 >>>>>>> ACTG content number of A's = 297,146,219 bp (27.67%) number of C's = 241,570,074 bp (22.5%) number of T's = 294,873,683 bp (27.46%) number of G's = 239,923,876 bp (22.35%) number of N's = 205,505 bp (0.02%) GC percentage = 44.84% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 6,678,975 number of insertions = 71,759 mapped reads with insertion percentage = 0.65% number of deletions = 57,904 mapped reads with deletion percentage = 0.52% homopolymer indels = 43.3% >>>>>>> Coverage mean coverageData = 0.3469X std coverageData = 16.9557X There is a 3.03% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 116948052 0.46919863842585974 22.82052169149295 chr2 243199373 65863988 0.27082301729453884 12.882197269589586 chr3 198022430 106753434 0.5390976870650461 15.278064077039023 chr4 191154276 46515954 0.24334247171117426 11.799379434883317 chr5 180915260 55759738 0.30820914719963366 15.410939289393234 chr6 171115067 77382725 0.45222624960313984 28.32060368042196 chr7 159138663 68564275 0.4308461168861272 23.54162590160556 chr8 146364022 51216255 0.34992380162933756 12.512483501256279 chr9 141213431 60944155 0.4315747770479424 13.608203875853421 chr10 135534747 35437663 0.2614655192443012 20.348873209064816 chr11 135006516 46998558 0.34812066404261555 14.87222790124784 chr12 133851895 63924580 0.4775769517495438 17.74125856763262 chr13 115169878 26600490 0.23096742361748443 17.8909475071902 chr14 107349540 25331422 0.23597140705027705 9.196577808304948 chr15 102531392 31102118 0.3033423948833153 21.446292594538285 chr16 90354753 41295557 0.45703801547661804 15.542393883096278 chr17 81195210 46712025 0.5753051811800228 25.637047679825834 chr18 78077248 17386824 0.22268745947603072 11.971238252943369 chr19 59128983 18138658 0.30676424791544277 7.496834447528784 chr20 63025520 16711971 0.2651619693102096 8.398663821507625 chr21 48129895 3382148 0.07027125240975489 3.468395911848008 chr22 51304566 12157705 0.23697120837159016 7.499474837789088 chrMT 16571 4022 0.24271317361655906 0.6879133427300569 chrX 155270560 37996262 0.2447100210110661 8.276477643519508 chrY 59373566 739527 0.012455492398755366 0.4980486254543662