BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237272.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 = 1,979,902 number of mapped reads = 1,808,955 (91.37%) number of supplementary alignments = 10,354 (0.52%) number of secondary alignments = 0 number of mapped bases = 127,489,731 bp number of sequenced bases = 127,423,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,269 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5972 >>>>>>> ACTG content number of A's = 38,401,548 bp (30.14%) number of C's = 24,208,752 bp (19%) number of T's = 39,190,592 bp (30.76%) number of G's = 25,620,100 bp (20.11%) number of N's = 2,373 bp (0%) GC percentage = 39.1% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,027,993 number of insertions = 10,747 mapped reads with insertion percentage = 0.59% number of deletions = 37,414 mapped reads with deletion percentage = 2.04% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.5159X There is a 3.39% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% 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 10740251 0.04309016746642328 0.8969492257401164 chr2 243199373 10779832 0.04432508138086359 0.44545452729820045 chr3 198022430 9172535 0.046320687005002414 0.25311603133012844 chr4 191154276 11107670 0.05810840454335429 0.3373158138176132 chr5 180915260 7259736 0.04012782559083186 0.24653213339491767 chr6 171115067 10863483 0.06348641993051378 0.6180592813806554 chr7 159138663 4467199 0.028071110538361126 0.26009117738097043 chr8 146364022 4450683 0.030408313048407482 1.2626117146132751 chr9 141213431 8830419 0.06253243007741947 0.5030981026916269 chr10 135534747 3438894 0.025372785032018393 0.4395565295785882 chr11 135006516 6581617 0.04875036550087701 0.37316978315534816 chr12 133851895 1584399 0.011836956062519697 0.15857890308078285 chr13 115169878 6070997 0.05271341001160043 0.2660096279836636 chr14 107349540 4317297 0.040217191429045715 0.294763137696174 chr15 102531392 3015138 0.02940697420747004 0.1958228844112523 chr16 90354753 2003148 0.02216981324712381 0.24767178933931894 chr17 81195210 2452510 0.030205106926874135 0.2343791161100932 chr18 78077248 3024255 0.03873413929753262 0.8682979522219633 chr19 59128983 1881641 0.031822651169224406 0.5139857513318312 chr20 63025520 1524505 0.024188693722796733 0.2073068396625669 chr21 48129895 2958660 0.06147239672972484 0.35295076416358917 chr22 51304566 1241374 0.024196169986117805 0.17559707569294003 chrMT 16571 32199 1.9430933558626515 1.849074884313559 chrX 155270560 9359998 0.06028185896927273 0.32633379286579267 chrY 59373566 331291 0.005579772655056629 0.21148146014888622