BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081735.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 = 2,770,227 number of mapped reads = 2,527,122 (91.22%) number of supplementary alignments = 16,866 (0.61%) number of secondary alignments = 0 number of mapped bases = 170,063,151 bp number of sequenced bases = 169,999,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,978 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0249 >>>>>>> ACTG content number of A's = 46,812,509 bp (27.54%) number of C's = 32,668,131 bp (19.22%) number of T's = 52,151,629 bp (30.68%) number of G's = 38,365,148 bp (22.57%) number of N's = 1,964 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,393,254 number of insertions = 12,117 mapped reads with insertion percentage = 0.48% number of deletions = 35,775 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.4522X There is a 4.63% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 13955311 0.055989072139563494 0.8050102489227047 chr2 243199373 15363724 0.06317337010568691 0.5873852097361676 chr3 198022430 10992318 0.05551046919280811 0.27633561115218674 chr4 191154276 11262832 0.058920115394122806 0.30253144332580756 chr5 180915260 9941926 0.05495349590742096 0.268325143487206 chr6 171115067 9726250 0.05684040669545482 0.33671141568271573 chr7 159138663 8833655 0.05550916938393532 0.5837976797337873 chr8 146364022 9250369 0.06320111236079588 0.5132304202013397 chr9 141213431 6862183 0.048594407425735585 0.4224121730312416 chr10 135534747 8532619 0.06295521398656538 0.5313024371183188 chr11 135006516 7345121 0.05440567772299228 0.40301604859351453 chr12 133851895 6898411 0.05153764165983604 0.2639117329168458 chr13 115169878 5438283 0.04721966450290066 0.24768596804668433 chr14 107349540 5113136 0.047630721100435085 0.2652292580401604 chr15 102531392 5274384 0.05144165018260944 0.26356318215009295 chr16 90354753 4324430 0.04786057021261516 0.3006221874694601 chr17 81195210 4809688 0.05923610518403733 0.31978881806242865 chr18 78077248 4944164 0.06332400445261595 0.7530919715838624 chr19 59128983 3401934 0.05753411994249927 0.6149386126680554 chr20 63025520 3490518 0.0553826132652297 0.27624785110403133 chr21 48129895 2160403 0.04488692526754941 0.2680208110364333 chr22 51304566 2024469 0.03945982117848926 0.22647513275900472 chrMT 16571 47075 2.840806227747269 2.211560090795002 chrX 155270560 9628706 0.06201243815955838 0.331948157800985 chrY 59373566 441242 0.007431623695972716 0.17714854314469416