BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234050.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 = 4,716,902 number of mapped reads = 4,419,303 (93.69%) number of supplementary alignments = 23,513 (0.5%) number of secondary alignments = 0 number of mapped bases = 278,025,707 bp number of sequenced bases = 277,888,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 448,135 duplication rate = 8.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4367 >>>>>>> ACTG content number of A's = 68,111,309 bp (24.51%) number of C's = 50,223,009 bp (18.07%) number of T's = 90,724,633 bp (32.65%) number of G's = 68,804,436 bp (24.76%) number of N's = 25,420 bp (0.01%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,783,655 number of insertions = 21,113 mapped reads with insertion percentage = 0.47% number of deletions = 82,181 mapped reads with deletion percentage = 1.84% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0898X std coverageData = 0.9096X There is a 6.85% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 26237244 0.10526450804710333 1.6260328275634734 chr2 243199373 15792546 0.06493662300683645 1.9788806093151534 chr3 198022430 32416102 0.16369914256682944 0.5315602299328644 chr4 191154276 9599055 0.0502162713848996 0.3191369160784527 chr5 180915260 18680556 0.10325583369805288 0.41318756285067304 chr6 171115067 23045638 0.13467918637462825 0.8888549279110503 chr7 159138663 14363279 0.09025637597571119 0.8803318317100544 chr8 146364022 9260116 0.06326770659527244 0.5050557270443394 chr9 141213431 11801007 0.08356858774998534 0.4881903103918968 chr10 135534747 10208308 0.07531875202452697 0.6499887342911574 chr11 135006516 14577325 0.10797497359312642 0.6295376226383311 chr12 133851895 8227416 0.06146656347300873 0.3248953152818216 chr13 115169878 14309579 0.12424758320921378 0.5647114670544288 chr14 107349540 9340916 0.08701402912392545 0.40069884913283105 chr15 102531392 5414431 0.05280754405441018 0.38437631012032697 chr16 90354753 8657413 0.09581580063640924 0.4546029075179527 chr17 81195210 8421060 0.10371375355762981 0.5000164816701441 chr18 78077248 5142621 0.06586580766781125 1.4128555196390602 chr19 59128983 10106570 0.17092413038796897 1.077895542154195 chr20 63025520 6497054 0.10308608322470009 0.4309827583243939 chr21 48129895 5051271 0.10495080032898473 0.43416355641925664 chr22 51304566 2983713 0.058156870482054174 0.3028601959960745 chrMT 16571 128222 7.737734596584394 9.095512645445574 chrX 155270560 7185956 0.04628022208459865 0.36087226532206446 chrY 59373566 578309 0.009740176293268288 0.28462433200524934