BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173939.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 7,496,252 number of mapped reads = 7,322,688 (97.68%) number of supplementary alignments = 994,515 (13.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,661,887 number of mapped paired reads (second in pair) = 3,660,801 number of mapped paired reads (both in pair) = 7,213,716 number of mapped paired reads (singletons) = 108,972 number of mapped bases = 829,464,866 bp number of sequenced bases = 828,879,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,954,206 duplication rate = 65.09% >>>>>>> Insert size mean insert size = 1,055,736.8281 std insert size = 9,548,252.7206 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.5377 >>>>>>> ACTG content number of A's = 246,593,129 bp (29.75%) number of C's = 165,152,106 bp (19.92%) number of T's = 244,717,897 bp (29.52%) number of G's = 172,410,069 bp (20.8%) number of N's = 6,156 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 7,239,445 number of insertions = 91,317 mapped reads with insertion percentage = 1.2% number of deletions = 247,228 mapped reads with deletion percentage = 3.29% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.2679X std coverageData = 4.972X There is a 5.54% of reference with a coverageData >= 1X There is a 4.19% of reference with a coverageData >= 2X There is a 3.17% of reference with a coverageData >= 3X There is a 2.56% of reference with a coverageData >= 4X There is a 1.94% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 1.22% of reference with a coverageData >= 7X There is a 1.05% of reference with a coverageData >= 8X There is a 0.8% of reference with a coverageData >= 9X There is a 0.72% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 63645898 0.255349004727254 2.353780119805746 chr2 243199373 75039194 0.30855011291497036 16.286845608189758 chr3 198022430 55909902 0.28234125800799437 1.6307558889403009 chr4 191154276 55068881 0.2880860535916026 2.302517515659368 chr5 180915260 50738729 0.2804557724981298 1.6294867289374326 chr6 171115067 48502147 0.28344755286803586 1.9340659385179912 chr7 159138663 47026092 0.2955038776466282 2.537447571290049 chr8 146364022 41974536 0.2867817884917101 2.5795871058812367 chr9 141213431 36107761 0.25569636502918763 2.2094946575409193 chr10 135534747 41003841 0.3025337923123138 2.658933025075725 chr11 135006516 38262323 0.2834109355136607 1.694488892196477 chr12 133851895 38100794 0.2846488949596119 1.7307563985084096 chr13 115169878 26823762 0.2329060555226081 1.4842864775383475 chr14 107349540 26528935 0.2471266760900885 1.558297422122467 chr15 102531392 24299244 0.23699321277136273 1.5281450210461485 chr16 90354753 25516625 0.28240490016059255 2.0806987356432503 chr17 81195210 23951178 0.2949826473753809 1.8444585306975187 chr18 78077248 23930540 0.30649825157771954 3.107884869368532 chr19 59128983 16886348 0.2855849558582802 1.96553104294713 chr20 63025520 18077719 0.28683173101943465 1.7227530728071336 chr21 48129895 12001338 0.24935308917669569 2.0040535839787315 chr22 51304566 10666698 0.20790933111099702 1.691590774257168 chrMT 16571 1468116 88.59549815943515 76.33588002527257 chrX 155270560 21565577 0.1388903150732502 1.1520976030699244 chrY 59373566 6368688 0.10726470429618461 1.695605041684265