BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524376.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 = 1,091,096 number of mapped reads = 1,005,098 (92.12%) number of supplementary alignments = 3,854 (0.35%) number of secondary alignments = 0 number of mapped bases = 58,866,790 bp number of sequenced bases = 58,850,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,286 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7574 >>>>>>> ACTG content number of A's = 15,210,197 bp (25.85%) number of C's = 11,473,228 bp (19.5%) number of T's = 18,332,396 bp (31.15%) number of G's = 13,826,721 bp (23.49%) number of N's = 7,567 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 286,256 number of insertions = 3,990 mapped reads with insertion percentage = 0.39% number of deletions = 10,507 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.2065X There is a 1.77% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4779248 0.019174467773943882 0.3943660818151678 chr2 243199373 5009609 0.020598774323320315 0.22828536679758973 chr3 198022430 3873957 0.01956322321668308 0.1468418338400548 chr4 191154276 3785779 0.019804835545504617 0.15929967633094042 chr5 180915260 3541018 0.019572798889380585 0.14754986339545872 chr6 171115067 3315573 0.019376277367790178 0.15857197875611068 chr7 159138663 3251278 0.020430472009181074 0.2760441712699573 chr8 146364022 2979767 0.020358602881246322 0.18995740222153035 chr9 141213431 2485996 0.017604529416185632 0.1716547791259028 chr10 135534747 2808161 0.02071912230743309 0.18719491992429435 chr11 135006516 2700126 0.01999996800154446 0.1843733712685427 chr12 133851895 2689009 0.020089435416659585 0.15296834768348508 chr13 115169878 1868685 0.01622546652346024 0.1338755557436274 chr14 107349540 1798040 0.016749396411013966 0.14076369456279902 chr15 102531392 1689253 0.016475471239091342 0.13483857073891028 chr16 90354753 1715222 0.018983196157926523 0.15146070589798766 chr17 81195210 1557364 0.019180491065913862 0.1546963482358328 chr18 78077248 1592823 0.020400603771280463 0.2953225109103701 chr19 59128983 1207280 0.020417736594590168 0.267114355821811 chr20 63025520 1264541 0.020063951872193994 0.15306429465711457 chr21 48129895 785832 0.01632731590210201 0.14411558862342805 chr22 51304566 687641 0.013403115036583684 0.12177354987754006 chrMT 16571 5239 0.31615472813952084 0.5713085164717253 chrX 155270560 3299720 0.021251420745825866 0.1672554428442615 chrY 59373566 175629 0.0029580335464438837 0.08755928410466068