BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504670.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 102,865,544 number of mapped reads = 102,226,327 (99.38%) number of supplementary alignments = 1,193,801 (1.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,271,318 number of mapped paired reads (second in pair) = 50,955,009 number of mapped paired reads (both in pair) = 101,867,384 number of mapped paired reads (singletons) = 358,943 number of mapped bases = 9,960,104,987 bp number of sequenced bases = 9,957,203,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,374,536 duplication rate = 21.89% >>>>>>> Insert size mean insert size = 34,459.0467 std insert size = 1,822,266.7849 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 51.1677 >>>>>>> ACTG content number of A's = 3,021,820,545 bp (30.35%) number of C's = 1,894,961,281 bp (19.03%) number of T's = 3,056,800,145 bp (30.7%) number of G's = 1,899,184,980 bp (19.07%) number of N's = 84,436,553 bp (0.85%) GC percentage = 38.1% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 108,685,374 number of insertions = 1,151,247 mapped reads with insertion percentage = 1.12% number of deletions = 1,232,757 mapped reads with deletion percentage = 1.19% homopolymer indels = 52.31% >>>>>>> Coverage mean coverageData = 3.2174X std coverageData = 169.3948X There is a 30.16% of reference with a coverageData >= 1X There is a 21.85% of reference with a coverageData >= 2X There is a 15.56% of reference with a coverageData >= 3X There is a 12.36% of reference with a coverageData >= 4X There is a 10.08% of reference with a coverageData >= 5X There is a 8.48% of reference with a coverageData >= 6X There is a 7.27% of reference with a coverageData >= 7X There is a 6.34% of reference with a coverageData >= 8X There is a 5.59% of reference with a coverageData >= 9X There is a 4.98% of reference with a coverageData >= 10X There is a 4.47% of reference with a coverageData >= 11X There is a 4.05% of reference with a coverageData >= 12X There is a 3.69% of reference with a coverageData >= 13X There is a 3.37% of reference with a coverageData >= 14X There is a 3.1% of reference with a coverageData >= 15X There is a 2.87% of reference with a coverageData >= 16X There is a 2.66% of reference with a coverageData >= 17X There is a 2.47% of reference with a coverageData >= 18X There is a 2.31% of reference with a coverageData >= 19X There is a 2.16% of reference with a coverageData >= 20X There is a 2.03% of reference with a coverageData >= 21X There is a 1.91% of reference with a coverageData >= 22X There is a 1.8% of reference with a coverageData >= 23X There is a 1.7% of reference with a coverageData >= 24X There is a 1.61% of reference with a coverageData >= 25X There is a 1.52% of reference with a coverageData >= 26X There is a 1.44% of reference with a coverageData >= 27X There is a 1.37% of reference with a coverageData >= 28X There is a 1.31% of reference with a coverageData >= 29X There is a 1.25% of reference with a coverageData >= 30X There is a 1.19% of reference with a coverageData >= 31X There is a 1.14% of reference with a coverageData >= 32X There is a 1.09% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 1% of reference with a coverageData >= 35X There is a 0.96% of reference with a coverageData >= 36X There is a 0.92% of reference with a coverageData >= 37X There is a 0.89% of reference with a coverageData >= 38X There is a 0.85% of reference with a coverageData >= 39X There is a 0.82% of reference with a coverageData >= 40X There is a 0.79% of reference with a coverageData >= 41X There is a 0.76% of reference with a coverageData >= 42X There is a 0.74% of reference with a coverageData >= 43X There is a 0.71% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.62% of reference with a coverageData >= 48X There is a 0.61% of reference with a coverageData >= 49X There is a 0.59% of reference with a coverageData >= 50X There is a 0.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 594075369 2.383445893200001 12.29816740676726 chr2 243199373 767646551 3.1564495480833332 24.449560232967453 chr3 198022430 1919813188 9.694927933163935 500.45468755367847 chr4 191154276 498398918 2.607312420256819 13.590541785039155 chr5 180915260 478536452 2.6450861690716416 17.352429445753558 chr6 171115067 436348977 2.550032470255819 40.03877789828842 chr7 159138663 444535819 2.793386664307969 13.719838173714276 chr8 146364022 1064401627 7.272290091891572 321.4490301739868 chr9 141213431 267987353 1.8977469147392927 9.656549962367881 chr10 135534747 312549482 2.306046891429251 12.378664465983835 chr11 135006516 310611399 2.3007141299757707 11.751780059281893 chr12 133851895 897958207 6.708595399415152 348.7979644913299 chr13 115169878 563233093 4.890454889602297 247.02370332643795 chr14 107349540 225303011 2.098779473111855 9.886045357582729 chr15 102531392 193644822 1.888639354472043 9.374134824390637 chr16 90354753 177191600 1.961065623188633 11.717502233676983 chr17 81195210 158413965 1.9510259903262765 21.20069345211398 chr18 78077248 175846091 2.2522065711127524 7.7622300018657 chr19 59128983 78872648 1.333908415099918 6.90180441437319 chr20 63025520 132209445 2.097712878846537 11.669548115789011 chr21 48129895 101297488 2.104668792649558 12.211129155654383 chr22 51304566 50950811 0.9931048047458388 8.345529487179926 chrMT 16571 7395 0.4462615412467564 2.2257575785656325 chrX 155270560 31776381 0.20465168026701264 13.538115262096719 chrY 59373566 78494895 1.3220512138347897 21.81349342558034