BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094161.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 42,512 number of mapped reads = 27,430 (64.52%) number of supplementary alignments = 72 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,767 number of mapped paired reads (second in pair) = 13,663 number of mapped paired reads (both in pair) = 26,858 number of mapped paired reads (singletons) = 572 number of mapped bases = 3,966,281 bp number of sequenced bases = 3,956,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,534 duplication rate = 35.43% >>>>>>> Insert size mean insert size = 103,841.3674 std insert size = 2,303,018.1426 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 12.7325 >>>>>>> ACTG content number of A's = 1,095,656 bp (27.69%) number of C's = 760,347 bp (19.22%) number of T's = 1,187,033 bp (30%) number of G's = 913,629 bp (23.09%) number of N's = 24 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0269 number of mismatches = 106,105 number of insertions = 378 mapped reads with insertion percentage = 1.28% number of deletions = 7,681 mapped reads with deletion percentage = 27.26% homopolymer indels = 55.63% >>>>>>> Coverage mean coverageData = 0.0013X std coverageData = 2.7358X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 32408 1.300217422527505E-4 0.14026739866730964 chr2 243199373 28447 1.1696987393137728E-4 0.10025854705376076 chr3 198022430 1303 6.580062672698239E-6 0.003241738386333962 chr4 191154276 343724 0.0017981496788489315 1.8595333755165007 chr5 180915260 1115 6.163106417888684E-6 0.0028995194451973843 chr6 171115067 16778 9.805097992919584E-5 0.09041071939004126 chr7 159138663 6499 4.083859872569119E-5 0.027232737811406265 chr8 146364022 2934 2.0045909916304432E-5 0.011027882168106152 chr9 141213431 28459 2.015318217146073E-4 0.12948082769424854 chr10 135534747 2360 1.74125089856109E-5 0.005654798026656828 chr11 135006516 2893 2.1428595342761084E-5 0.010847826712423169 chr12 133851895 1726 1.2894849191339428E-5 0.005131755177691147 chr13 115169878 9100 7.901371572174454E-5 0.03999527586576468 chr14 107349540 2515 2.3428139515083158E-5 0.012587472850168088 chr15 102531392 9269 9.040158159561512E-5 0.05837057485178944 chr16 90354753 2878 3.185222585910893E-5 0.016618575266270898 chr17 81195210 5374 6.618617034182189E-5 0.032131117989154634 chr18 78077248 2367 3.0316129994745717E-5 0.019446414238754116 chr19 59128983 1629 2.754994111770872E-5 0.012997500005520142 chr20 63025520 248 3.934913984049635E-6 0.0022249404876995486 chr21 48129895 2357 4.8971642261010545E-5 0.04184828803762417 chr22 51304566 620 1.2084694372036984E-5 0.008231166880443576 chrMT 16571 3376818 203.7787701406071 1146.2597072652886 chrX 155270560 84140 5.418928095577165E-4 0.5008237921450428 chrY 59373566 320 5.389603851653445E-6 0.0032677398279634673