BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238079.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,833,864 number of mapped reads = 1,637,450 (89.29%) number of supplementary alignments = 10,054 (0.55%) number of secondary alignments = 0 number of mapped bases = 108,509,848 bp number of sequenced bases = 108,460,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,895 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4872 >>>>>>> ACTG content number of A's = 29,649,060 bp (27.34%) number of C's = 20,288,199 bp (18.71%) number of T's = 32,970,555 bp (30.4%) number of G's = 25,343,068 bp (23.37%) number of N's = 210,007 bp (0.19%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,026,666 number of insertions = 10,299 mapped reads with insertion percentage = 0.62% number of deletions = 29,086 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.445X There is a 3.1% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8594797 0.034482549995331804 0.7971175710694484 chr2 243199373 9433842 0.038790568756935075 0.5954087632950014 chr3 198022430 7029732 0.035499675466057055 0.2142121166593222 chr4 191154276 7021077 0.036729897687457436 0.24941421068719674 chr5 180915260 6404622 0.035401225966234136 0.20830887233154294 chr6 171115067 6226087 0.036385381539779896 0.3028605348652033 chr7 159138663 6154384 0.03867309102628316 0.608020352819553 chr8 146364022 5569990 0.038055732029555735 0.39391621803889276 chr9 141213431 4501670 0.031878483286763286 0.4998268521562797 chr10 135534747 5339937 0.03939902584537971 0.5538477854697802 chr11 135006516 4884831 0.03618218693977704 0.3661670126482722 chr12 133851895 4917534 0.03673862069715188 0.22040366188477584 chr13 115169878 3255073 0.02826323216214573 0.17926076938535965 chr14 107349540 3198103 0.02979149235292485 0.24763586198732224 chr15 102531392 3056369 0.02980910470814636 0.18866666207616925 chr16 90354753 3114219 0.03446657642902305 0.2704798323796317 chr17 81195210 2984508 0.03675719294278566 0.27152706395659354 chr18 78077248 2991248 0.03831139130313609 0.961113996532869 chr19 59128983 2362500 0.03995502510164939 0.5719004798107332 chr20 63025520 2204292 0.03497459441826105 0.23283830160886693 chr21 48129895 1447053 0.03006557566768014 0.23802633304713705 chr22 51304566 1193977 0.02327233408426065 0.16330195601471667 chrMT 16571 83357 5.030293886910869 3.7038543961023054 chrX 155270560 6185452 0.03983660521350602 0.2877403714748498 chrY 59373566 355194 0.005982359220263105 0.17438870258273326