BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080910.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,895,997 number of mapped reads = 3,530,986 (90.63%) number of supplementary alignments = 36,263 (0.93%) number of secondary alignments = 0 number of mapped bases = 242,196,962 bp number of sequenced bases = 242,105,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,549 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8269 >>>>>>> ACTG content number of A's = 69,740,992 bp (28.81%) number of C's = 42,862,596 bp (17.7%) number of T's = 77,808,544 bp (32.14%) number of G's = 50,533,506 bp (20.87%) number of N's = 1,159,582 bp (0.48%) GC percentage = 38.58% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 2,826,798 number of insertions = 19,261 mapped reads with insertion percentage = 0.54% number of deletions = 55,666 mapped reads with deletion percentage = 1.56% homopolymer indels = 50.12% >>>>>>> Coverage mean coverageData = 0.0782X std coverageData = 0.5859X There is a 5.89% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17955163 0.07203658280955698 1.0596223186238956 chr2 243199373 23056945 0.09480676169341934 0.5523716729409229 chr3 198022430 16872979 0.08520741311981678 0.36629496408415324 chr4 191154276 17150672 0.08972162359580176 0.39703058029004346 chr5 180915260 14796019 0.08178425081444207 0.3622351943225222 chr6 171115067 14177254 0.08285216637293547 0.43820623947522214 chr7 159138663 12820556 0.0805621698606328 0.7962318005108686 chr8 146364022 12279101 0.08389425783885605 1.0865256570924477 chr9 141213431 10263731 0.07268239945249967 0.5219959208994815 chr10 135534747 11123287 0.08206963340552073 0.49759195040091697 chr11 135006516 11160248 0.08266451376317273 0.47383030635553347 chr12 133851895 10699021 0.07993178579952118 0.36209458187312454 chr13 115169878 8602418 0.07469329784303497 0.344377031432834 chr14 107349540 7346045 0.06843108037537934 0.3602400271303381 chr15 102531392 6624798 0.06461238719942473 0.3181595639872508 chr16 90354753 6226089 0.06890715533249259 0.3595396903877093 chr17 81195210 5852543 0.07207990471359087 0.3985435477451262 chr18 78077248 6371315 0.08160270966517673 0.9135524065423848 chr19 59128983 3804937 0.06434977919373314 0.6663176412832763 chr20 63025520 4273450 0.06780507324651983 0.3466802933343758 chr21 48129895 3388707 0.07040752945752322 0.358668027930972 chr22 51304566 2202316 0.04292631575910807 0.2554510546188932 chrMT 16571 13948 0.8417114235712992 1.0692215545389128 chrX 155270560 14587532 0.09394911694786184 0.42556437129634805 chrY 59373566 547888 0.009227810234608445 0.17812103260724507