BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230401.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 = 2,674,596 number of mapped reads = 2,324,490 (86.91%) number of supplementary alignments = 26,396 (0.99%) number of secondary alignments = 0 number of mapped bases = 150,774,241 bp number of sequenced bases = 150,714,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 202,211 duplication rate = 6.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7286 >>>>>>> ACTG content number of A's = 41,636,466 bp (27.63%) number of C's = 27,332,588 bp (18.14%) number of T's = 48,019,052 bp (31.86%) number of G's = 33,647,977 bp (22.33%) number of N's = 77,973 bp (0.05%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,332,472 number of insertions = 12,480 mapped reads with insertion percentage = 0.53% number of deletions = 37,115 mapped reads with deletion percentage = 1.58% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.4682X There is a 3.54% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 12274083 0.04924394150255698 0.8403243127385118 chr2 243199373 11478736 0.04719887168459106 0.5106659017643412 chr3 198022430 9585968 0.04840849594664604 0.2865371307699883 chr4 191154276 9926203 0.05192770576578679 0.3250061186964066 chr5 180915260 10099802 0.05582614755659639 0.3101440308122316 chr6 171115067 8519035 0.04978541720116324 0.3393348493595301 chr7 159138663 7742681 0.0486536763225163 0.5312537372057481 chr8 146364022 8023502 0.05481881332831917 0.7187485709776824 chr9 141213431 5868456 0.04155735016451799 0.4059713915459824 chr10 135534747 6726949 0.049632652503494176 0.44507145105055096 chr11 135006516 7066226 0.052339888542861146 0.4134377315307847 chr12 133851895 7540040 0.056331215930861496 0.31746953813421563 chr13 115169878 5403210 0.04691513174998761 0.2862677555999433 chr14 107349540 4546404 0.04235140644291536 0.28473065929165514 chr15 102531392 4012789 0.039137174690849805 0.2577568652112278 chr16 90354753 3739592 0.04138788360143046 0.29820672507623075 chr17 81195210 3673006 0.045236732560947866 0.30118998865504243 chr18 78077248 4257169 0.05452509033105265 0.8063981926337452 chr19 59128983 2229389 0.03770382791802795 0.5518619236037577 chr20 63025520 2812086 0.044618211797379854 0.2943523860193446 chr21 48129895 1915596 0.03980054392389595 0.2797492051530319 chr22 51304566 1396145 0.02721288003878641 0.20827440840797212 chrMT 16571 338087 20.40232937058717 16.6767365913518 chrX 155270560 11144985 0.07177783734405285 0.3970924640506167 chrY 59373566 454102 0.007648218400761039 0.1663346171163438