BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504668.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 = 123,351,530 number of mapped reads = 122,775,572 (99.53%) number of supplementary alignments = 1,326,382 (1.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 61,471,167 number of mapped paired reads (second in pair) = 61,304,405 number of mapped paired reads (both in pair) = 122,556,994 number of mapped paired reads (singletons) = 218,578 number of mapped bases = 11,656,337,410 bp number of sequenced bases = 11,652,891,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,167,891 duplication rate = 27.45% >>>>>>> Insert size mean insert size = 31,806.0231 std insert size = 1,745,250.1643 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 51.2342 >>>>>>> ACTG content number of A's = 3,558,436,868 bp (30.54%) number of C's = 2,250,584,433 bp (19.31%) number of T's = 3,596,089,056 bp (30.86%) number of G's = 2,238,169,244 bp (19.21%) number of N's = 9,611,876 bp (0.08%) GC percentage = 38.52% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 61,978,300 number of insertions = 1,356,998 mapped reads with insertion percentage = 1.1% number of deletions = 1,466,833 mapped reads with deletion percentage = 1.18% homopolymer indels = 52.13% >>>>>>> Coverage mean coverageData = 3.7653X std coverageData = 196.9627X There is a 32.57% of reference with a coverageData >= 1X There is a 23.75% of reference with a coverageData >= 2X There is a 17.24% of reference with a coverageData >= 3X There is a 13.82% of reference with a coverageData >= 4X There is a 11.38% of reference with a coverageData >= 5X There is a 9.66% of reference with a coverageData >= 6X There is a 8.34% of reference with a coverageData >= 7X There is a 7.31% of reference with a coverageData >= 8X There is a 6.49% of reference with a coverageData >= 9X There is a 5.81% of reference with a coverageData >= 10X There is a 5.24% of reference with a coverageData >= 11X There is a 4.76% of reference with a coverageData >= 12X There is a 4.35% of reference with a coverageData >= 13X There is a 4% of reference with a coverageData >= 14X There is a 3.69% of reference with a coverageData >= 15X There is a 3.42% of reference with a coverageData >= 16X There is a 3.18% of reference with a coverageData >= 17X There is a 2.96% of reference with a coverageData >= 18X There is a 2.77% of reference with a coverageData >= 19X There is a 2.6% of reference with a coverageData >= 20X There is a 2.45% of reference with a coverageData >= 21X There is a 2.31% of reference with a coverageData >= 22X There is a 2.18% of reference with a coverageData >= 23X There is a 2.06% of reference with a coverageData >= 24X There is a 1.95% of reference with a coverageData >= 25X There is a 1.86% of reference with a coverageData >= 26X There is a 1.77% of reference with a coverageData >= 27X There is a 1.68% of reference with a coverageData >= 28X There is a 1.6% of reference with a coverageData >= 29X There is a 1.53% of reference with a coverageData >= 30X There is a 1.47% of reference with a coverageData >= 31X There is a 1.4% of reference with a coverageData >= 32X There is a 1.34% of reference with a coverageData >= 33X There is a 1.29% of reference with a coverageData >= 34X There is a 1.24% of reference with a coverageData >= 35X There is a 1.19% of reference with a coverageData >= 36X There is a 1.15% of reference with a coverageData >= 37X There is a 1.1% of reference with a coverageData >= 38X There is a 1.06% of reference with a coverageData >= 39X There is a 1.02% of reference with a coverageData >= 40X There is a 0.99% of reference with a coverageData >= 41X There is a 0.95% of reference with a coverageData >= 42X There is a 0.92% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.86% of reference with a coverageData >= 45X There is a 0.84% of reference with a coverageData >= 46X There is a 0.81% of reference with a coverageData >= 47X There is a 0.78% of reference with a coverageData >= 48X There is a 0.76% of reference with a coverageData >= 49X There is a 0.74% of reference with a coverageData >= 50X There is a 0.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 695881628 2.7918952627203284 14.326802880125818 chr2 243199373 902119726 3.7093834366094356 28.788494963422693 chr3 198022430 2241641242 11.320138036888043 583.2680167661953 chr4 191154276 582844892 3.049081109752418 15.773420859013141 chr5 180915260 560622772 3.0988141741056006 20.159195429950575 chr6 171115067 512223996 2.993447654729317 47.23947462058545 chr7 159138663 520757421 3.2723501076542285 15.927172721580693 chr8 146364022 1241370487 8.481390918596102 373.6932687845491 chr9 141213431 314479641 2.226981093604333 11.14753812476873 chr10 135534747 366898848 2.7070463930552067 14.399260536904578 chr11 135006516 363727694 2.694149177214528 13.730795497973826 chr12 133851895 1045589265 7.81153875333629 403.11651479383477 chr13 115169878 655912939 5.695177857182413 286.16852939075136 chr14 107349540 264097756 2.460166629498366 11.551155465583728 chr15 102531392 227253804 2.216431471056201 10.929193985960561 chr16 90354753 208739047 2.3102165638148553 13.773640139241682 chr17 81195210 186643725 2.2987036427395164 24.97007949064389 chr18 78077248 205992802 2.638320474615089 9.03987221125269 chr19 59128983 93334972 1.5784978408980923 8.000735858273808 chr20 63025520 155508192 2.467384513447886 13.622093910992787 chr21 48129895 118496185 2.4620079682284786 14.230675508794732 chr22 51304566 60268639 1.1747227137639171 9.855781489695786 chrMT 16571 9522 0.5746183090942008 2.5544163351727143 chrX 155270560 39924998 0.2571317962658214 17.048108195688638 chrY 59373566 91997217 1.5494642346393679 26.001926386870032