BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238517.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 = 3,586,694 number of mapped reads = 2,498,644 (69.66%) number of supplementary alignments = 24,079 (0.67%) number of secondary alignments = 0 number of mapped bases = 153,490,657 bp number of sequenced bases = 153,426,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,027,995 duplication rate = 21.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9314 >>>>>>> ACTG content number of A's = 38,030,529 bp (24.79%) number of C's = 27,089,694 bp (17.66%) number of T's = 51,240,012 bp (33.4%) number of G's = 37,056,455 bp (24.15%) number of N's = 10,133 bp (0.01%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 896,506 number of insertions = 9,540 mapped reads with insertion percentage = 0.38% number of deletions = 37,689 mapped reads with deletion percentage = 1.5% homopolymer indels = 41.99% >>>>>>> Coverage mean coverageData = 0.0496X std coverageData = 0.9479X There is a 1.38% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 16218120 0.06506752093508325 1.1982394738485418 chr2 243199373 12391763 0.05095310422531393 1.8857094891783317 chr3 198022430 9015998 0.0455301856461412 0.6306770455275823 chr4 191154276 8085472 0.042298148747663904 0.6018876393171481 chr5 180915260 9359729 0.051735431273182815 0.6624098829331525 chr6 171115067 9496161 0.05549576180804698 0.8885244002160236 chr7 159138663 8894493 0.05589146491698249 0.8480930424540224 chr8 146364022 7364200 0.050314277370705214 0.7369379416621147 chr9 141213431 6264503 0.044361948829074196 0.648601270227012 chr10 135534747 6697891 0.049418257297517955 0.6913808608053632 chr11 135006516 6651087 0.04926493325699924 0.676366417357119 chr12 133851895 5984031 0.04470635996599077 0.6307142402282591 chr13 115169878 4073501 0.03536950000068594 0.6904347265453529 chr14 107349540 4055065 0.037774404995121545 0.5661833682945501 chr15 102531392 3831112 0.03736525882726726 0.6097425047882719 chr16 90354753 5034363 0.055717744035003895 0.7197413670640025 chr17 81195210 4322707 0.053238448425713784 0.7055270309042975 chr18 78077248 5045679 0.06462419116001629 2.1029033049581964 chr19 59128983 2922382 0.04942385022925221 0.8992184289906804 chr20 63025520 3401946 0.05397727777573275 0.698340015685011 chr21 48129895 2104522 0.0437258797261037 0.5907668320789019 chr22 51304566 1247205 0.02430982458754256 0.4649457390526863 chrMT 16571 38174 2.3036630257679076 4.5550216435516235 chrX 155270560 10480530 0.06749850068164887 0.7600871464911924 chrY 59373566 510023 0.008590068516349515 0.32143295365450175