BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926975.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 = 24,704,816 number of mapped reads = 24,396,698 (98.75%) number of supplementary alignments = 115,093 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,251,591 number of mapped paired reads (second in pair) = 12,145,107 number of mapped paired reads (both in pair) = 24,220,652 number of mapped paired reads (singletons) = 176,046 number of mapped bases = 2,344,650,457 bp number of sequenced bases = 2,342,877,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,778,246 duplication rate = 5.56% >>>>>>> Insert size mean insert size = 57,515.2064 std insert size = 2,463,388.5571 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.4071 >>>>>>> ACTG content number of A's = 651,300,135 bp (27.8%) number of C's = 494,803,120 bp (21.12%) number of T's = 657,146,269 bp (28.05%) number of G's = 539,417,723 bp (23.02%) number of N's = 209,785 bp (0.01%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 22,705,697 number of insertions = 374,102 mapped reads with insertion percentage = 1.51% number of deletions = 1,268,372 mapped reads with deletion percentage = 5.06% homopolymer indels = 52.93% >>>>>>> Coverage mean coverageData = 0.7574X std coverageData = 3.7244X There is a 24.27% of reference with a coverageData >= 1X There is a 14.57% of reference with a coverageData >= 2X There is a 9.36% of reference with a coverageData >= 3X There is a 6.4% of reference with a coverageData >= 4X There is a 4.54% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.47% of reference with a coverageData >= 7X There is a 1.88% of reference with a coverageData >= 8X There is a 1.45% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 0.9% of reference with a coverageData >= 11X There is a 0.72% of reference with a coverageData >= 12X There is a 0.58% of reference with a coverageData >= 13X There is a 0.47% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 323106513 1.2963117672633602 5.8078145094182 chr2 243199373 163698219 0.6731029647843706 4.397426520074968 chr3 198022430 127163850 0.6421689199551788 1.8990918420425682 chr4 191154276 92849848 0.4857325190047017 1.9108529659739002 chr5 180915260 174155311 0.9626347219134528 2.2856820809598952 chr6 171115067 68682846 0.40138397631577355 2.5745912633035966 chr7 159138663 95822379 0.6021313563505306 2.8609241158163328 chr8 146364022 167989977 1.1477545827484845 2.9661046944617238 chr9 141213431 128346736 0.9088847646510338 6.151879301591936 chr10 135534747 88599200 0.6537010025923463 5.076350498960857 chr11 135006516 131628152 0.974976289292585 4.144559138498783 chr12 133851895 107181412 0.8007463174129884 2.30412624705927 chr13 115169878 32856199 0.28528465576737 1.2152517552159128 chr14 107349540 115022494 1.0714763565824315 2.6783969566987413 chr15 102531392 56516113 0.5512078973822964 1.8256777860300795 chr16 90354753 48541797 0.5372356781275247 2.7343472750031452 chr17 81195210 113858836 1.4022851348004395 5.475524472949754 chr18 78077248 42956250 0.5501762818279661 5.885135262352332 chr19 59128983 34491389 0.5833245770521709 3.413725996268225 chr20 63025520 60570644 0.9610494923326297 2.6455453985314787 chr21 48129895 12926719 0.2685798296464183 2.3490074516233124 chr22 51304566 37400267 0.7289851550444847 2.202957692021596 chrMT 16571 4553292 274.77472693259307 210.82308526967094 chrX 155270560 111389652 0.7173906759916368 2.2398064749217728 chrY 59373566 4342362 0.07313628425147986 1.2896096201377094