BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524393.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 6,567,832 number of mapped reads = 6,069,104 (92.41%) number of supplementary alignments = 23,649 (0.36%) number of secondary alignments = 0 number of mapped bases = 355,261,605 bp number of sequenced bases = 355,163,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 588,124 duplication rate = 7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8889 >>>>>>> ACTG content number of A's = 88,431,263 bp (24.9%) number of C's = 63,384,076 bp (17.85%) number of T's = 116,503,988 bp (32.8%) number of G's = 86,799,138 bp (24.44%) number of N's = 44,564 bp (0.01%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,725,262 number of insertions = 27,638 mapped reads with insertion percentage = 0.45% number of deletions = 61,724 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.1148X std coverageData = 0.9911X There is a 8.46% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 28291544 0.11350641328993921 2.1838577915834883 chr2 243199373 30569173 0.12569593672431056 1.1489645676127653 chr3 198022430 24021159 0.1213052430474669 0.4527036925740072 chr4 191154276 22468725 0.11754236143794136 0.5926249236085243 chr5 180915260 21997532 0.12159025170126611 0.4550492840824415 chr6 171115067 21481885 0.1255405814147272 0.6080921424345355 chr7 159138663 20939673 0.13158130529222808 1.5738464257661362 chr8 146364022 18030100 0.12318669406338123 0.8078924047171351 chr9 141213431 14789503 0.1047315605553129 0.7460135784616105 chr10 135534747 16910173 0.12476633021641306 0.8468265108466297 chr11 135006516 16740128 0.12399496332458501 0.8740896425596003 chr12 133851895 16428050 0.12273304012617826 0.5003835622121973 chr13 115169878 10662596 0.09258146474723192 0.3952224033710954 chr14 107349540 10845596 0.10103067046211842 0.4627760571942144 chr15 102531392 9526176 0.09290984755186002 0.404412254283744 chr16 90354753 10425602 0.11538520834648289 0.5085881785852477 chr17 81195210 9823137 0.12098173032621012 0.5676323867610789 chr18 78077248 8830028 0.11309348403263393 1.597714367443861 chr19 59128983 7295490 0.12338263961008766 1.38273072234581 chr20 63025520 7534240 0.11954268683542793 0.4814001633203192 chr21 48129895 4584143 0.09524523167981147 0.5223888307300921 chr22 51304566 4230597 0.08246043831654282 0.3722608296982441 chrMT 16571 117447 7.08750226298956 5.130921563429325 chrX 155270560 17695362 0.11396469491705317 0.5877120193527027 chrY 59373566 1023546 0.01723908582482649 0.4083083863827332