BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124813.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 29,954,254 number of mapped reads = 29,437,559 (98.28%) number of supplementary alignments = 99,197 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,745,395 number of mapped paired reads (second in pair) = 14,692,164 number of mapped paired reads (both in pair) = 29,328,756 number of mapped paired reads (singletons) = 108,803 number of mapped bases = 2,567,494,608 bp number of sequenced bases = 2,566,088,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,553,546 duplication rate = 13.48% >>>>>>> Insert size mean insert size = 35,817.2617 std insert size = 1,792,200.1891 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.8308 >>>>>>> ACTG content number of A's = 715,339,647 bp (27.88%) number of C's = 487,218,112 bp (18.99%) number of T's = 755,001,470 bp (29.42%) number of G's = 608,507,974 bp (23.71%) number of N's = 21,690 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 18,942,495 number of insertions = 330,418 mapped reads with insertion percentage = 1.09% number of deletions = 835,989 mapped reads with deletion percentage = 2.78% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.8294X std coverageData = 6.3295X There is a 28.2% of reference with a coverageData >= 1X There is a 16.32% of reference with a coverageData >= 2X There is a 10.1% of reference with a coverageData >= 3X There is a 6.73% of reference with a coverageData >= 4X There is a 4.65% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 1.81% of reference with a coverageData >= 8X There is a 1.37% of reference with a coverageData >= 9X There is a 1.05% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.65% of reference with a coverageData >= 12X There is a 0.52% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193751218 0.7773349459378077 6.500268604332779 chr2 243199373 233018930 0.958139517900813 8.971161997749935 chr3 198022430 204488523 1.0326533362912473 2.4069222608076224 chr4 191154276 148172397 0.7751456054271054 4.383873358536288 chr5 180915260 163776440 0.9052660344959292 2.4128095748199248 chr6 171115067 136370312 0.796950931270126 4.842614383847917 chr7 159138663 180151769 1.1320427456400084 9.491577922200664 chr8 146364022 132475316 0.9051084698943296 2.9193634140161517 chr9 141213431 88376226 0.6258344222229116 6.768371263838024 chr10 135534747 121465644 0.8961956006750063 16.050599565819706 chr11 135006516 139048939 1.0299424288528414 4.767870847145218 chr12 133851895 122896895 0.9181558094489436 2.26512080456233 chr13 115169878 73790105 0.6407066351151297 1.8096507254230083 chr14 107349540 51812920 0.4826561902361203 2.0396894416490063 chr15 102531392 85223021 0.8311895443690065 2.2810400317861705 chr16 90354753 72125398 0.7982468614573048 6.646592590229055 chr17 81195210 68598722 0.8448616858063425 8.647592062434079 chr18 78077248 62715600 0.8032506473588823 8.060627221383243 chr19 59128983 28260425 0.47794539270191744 4.308608928220197 chr20 63025520 64731771 1.0270723827427366 2.794168753467312 chr21 48129895 36039712 0.7488009687118578 2.932784581909771 chr22 51304566 23303195 0.4542128862370651 1.8973173569174009 chrMT 16571 527839 31.853177237342344 21.196895319626034 chrX 155270560 129775802 0.8358043018586395 3.3340685681665403 chrY 59373566 6597489 0.11111828789262886 6.825221056436776