BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,326,987 number of mapped reads = 1,212,108 (91.34%) number of supplementary alignments = 6,245 (0.47%) number of secondary alignments = 0 number of mapped bases = 70,356,247 bp number of sequenced bases = 70,335,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,731 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8491 >>>>>>> ACTG content number of A's = 18,406,625 bp (26.17%) number of C's = 12,758,844 bp (18.14%) number of T's = 22,855,101 bp (32.49%) number of G's = 16,305,908 bp (23.18%) number of N's = 8,760 bp (0.01%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 343,015 number of insertions = 5,153 mapped reads with insertion percentage = 0.42% number of deletions = 13,175 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.234X There is a 2.1% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 5685204 0.022809186902687798 0.4313484023605545 chr2 243199373 4609029 0.018951648366297393 0.23986714725615366 chr3 198022430 5028515 0.025393663737991703 0.1677942605368794 chr4 191154276 3846133 0.020120570046782527 0.16154927045443873 chr5 180915260 4290434 0.023715158135361274 0.16357592358986345 chr6 171115067 4577426 0.026750572467122372 0.18679662792584117 chr7 159138663 3224361 0.020261330208611844 0.3093800016639996 chr8 146364022 7685673 0.05251067096256756 0.32144175023093946 chr9 141213431 2930300 0.020750859031248948 0.20283858551997325 chr10 135534747 3505555 0.02586462200722594 0.22370661309909612 chr11 135006516 2996131 0.02219249180535849 0.20260420891552564 chr12 133851895 2791584 0.02085576748838707 0.15560611243667555 chr13 115169878 1872471 0.016258339702330846 0.13547975757895725 chr14 107349540 1498151 0.013955821329089999 0.13401127639459823 chr15 102531392 2123930 0.020714924069303576 0.15414482375299568 chr16 90354753 2234452 0.02472976712138209 0.17396948237698218 chr17 81195210 1965900 0.024212019403607676 0.1822920117473938 chr18 78077248 1677070 0.02147962489661521 0.33687671231323085 chr19 59128983 1065421 0.01801859166087805 0.3229535486907898 chr20 63025520 1521597 0.024142553683016023 0.165867821617644 chr21 48129895 1039560 0.02159904982132207 0.16294032306298573 chr22 51304566 437640 0.008530234911255267 0.09695391646146422 chrMT 16571 3626 0.21881600386216885 0.4989018881093472 chrX 155270560 3569304 0.022987641701041072 0.1789339191099509 chrY 59373566 176780 0.0029774192777977998 0.08060179271605723