BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013300.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 = 3,072,991 number of mapped reads = 2,772,166 (90.21%) number of supplementary alignments = 29,639 (0.96%) number of secondary alignments = 0 number of mapped bases = 179,927,927 bp number of sequenced bases = 179,843,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,628 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2113 >>>>>>> ACTG content number of A's = 49,776,111 bp (27.68%) number of C's = 34,922,156 bp (19.42%) number of T's = 53,722,843 bp (29.87%) number of G's = 41,402,679 bp (23.02%) number of N's = 19,910 bp (0.01%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,412,643 number of insertions = 13,326 mapped reads with insertion percentage = 0.48% number of deletions = 48,019 mapped reads with deletion percentage = 1.71% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.0581X std coverageData = 0.5674X There is a 5.07% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12987603 0.05210660237432267 0.8068479607403617 chr2 243199373 21362999 0.08784150524927546 0.7678734428423023 chr3 198022430 16023997 0.08092011091874794 0.31437446344263237 chr4 191154276 8255917 0.04318981072649403 0.2742298074171014 chr5 180915260 8885521 0.04911427040482931 0.24722637926771487 chr6 171115067 13089059 0.07649273222678865 0.5253678964294055 chr7 159138663 12905564 0.08109634551849917 1.265619596211633 chr8 146364022 8972045 0.061299524824481796 0.4494250565974201 chr9 141213431 7686173 0.0544294756211964 0.5331171560359749 chr10 135534747 4839265 0.035704976820445905 0.5775209940943601 chr11 135006516 6813146 0.050465312355738444 0.428055893048049 chr12 133851895 8174387 0.06107038678832302 0.28541241471484435 chr13 115169878 3833131 0.033282409138264434 0.1987564695909959 chr14 107349540 7435219 0.06926176861121155 0.34194549084355913 chr15 102531392 1698213 0.016562859109530086 0.16322325609201385 chr16 90354753 3660201 0.04050922478865058 0.2957893086064843 chr17 81195210 5910529 0.07279406014221775 0.34163494160873326 chr18 78077248 5684883 0.07281100635104353 1.1102061486698147 chr19 59128983 2844042 0.04809895005297148 0.6311338886973317 chr20 63025520 3590914 0.05697555529886941 0.27434981845654194 chr21 48129895 2379868 0.04944677315419034 0.2855776796154186 chr22 51304566 2538463 0.049478305693103415 0.24454744716228166 chrMT 16571 162210 9.788787641059683 5.7139652405090615 chrX 155270560 9781542 0.0629967586901213 0.3485347876021094 chrY 59373566 413036 0.0069565638014735375 0.19827458429182646