BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084789.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 = 2,357,537 number of mapped reads = 2,123,423 (90.07%) number of supplementary alignments = 20,295 (0.86%) number of secondary alignments = 0 number of mapped bases = 143,056,768 bp number of sequenced bases = 142,997,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,739 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7066 >>>>>>> ACTG content number of A's = 39,750,995 bp (27.8%) number of C's = 27,304,332 bp (19.09%) number of T's = 44,262,647 bp (30.95%) number of G's = 31,622,684 bp (22.11%) number of N's = 57,262 bp (0.04%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,257,515 number of insertions = 11,068 mapped reads with insertion percentage = 0.52% number of deletions = 35,997 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.3835X There is a 3.94% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12090187 0.0485061459485792 0.6260409865098803 chr2 243199373 12337604 0.05073041039460246 0.4775418293223475 chr3 198022430 10292955 0.05197873291424613 0.25787687119022074 chr4 191154276 8233376 0.04307189026731476 0.2551690516047644 chr5 180915260 8994356 0.04971585039316197 0.25510609165151155 chr6 171115067 8667695 0.05065418932395942 0.3224002538161401 chr7 159138663 7989057 0.05020186075083464 0.4678358869635284 chr8 146364022 6773247 0.04627672092804337 0.37456942409273486 chr9 141213431 5676038 0.0401947460649122 0.36034400597974975 chr10 135534747 6268349 0.04624901834213775 0.3689971374014639 chr11 135006516 7262670 0.05379495905219864 0.3800289860784679 chr12 133851895 6874231 0.05135699423605471 0.2614055449760881 chr13 115169878 4937982 0.042875638020559506 0.2362772186218135 chr14 107349540 4416618 0.04114240265957358 0.26004321922435025 chr15 102531392 4084115 0.03983282505322858 0.23222620224053753 chr16 90354753 3736912 0.04135822273787855 0.27216771098127757 chr17 81195210 4067296 0.05009280719884831 0.2997703452988227 chr18 78077248 4148675 0.05313551778874173 0.8524988489693031 chr19 59128983 2823131 0.047745299458304566 0.5001823192038297 chr20 63025520 2523655 0.04004179576780961 0.244884991829743 chr21 48129895 1903276 0.03954456996010484 0.2421995629753788 chr22 51304566 1667750 0.03250685328865271 0.2029777509815103 chrMT 16571 14619 0.8822038500995716 1.1359801508422138 chrX 155270560 6948892 0.0447534419918367 0.2724108072439454 chrY 59373566 324082 0.005458354985786099 0.1319227888881594