BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514727.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 42,865,081 number of mapped reads = 41,958,639 (97.89%) number of supplementary alignments = 1,125,122 (2.62%) number of secondary alignments = 0 number of mapped bases = 4,026,021,895 bp number of sequenced bases = 4,024,183,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,651,707 duplication rate = 43.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6004 >>>>>>> ACTG content number of A's = 1,077,989,815 bp (26.79%) number of C's = 917,532,557 bp (22.8%) number of T's = 1,087,558,941 bp (27.03%) number of G's = 919,053,424 bp (22.84%) number of N's = 22,049,257 bp (0.55%) GC percentage = 45.64% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 37,140,289 number of insertions = 1,405,285 mapped reads with insertion percentage = 3.24% number of deletions = 1,020,075 mapped reads with deletion percentage = 2.37% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 1.3005X std coverageData = 34.0651X There is a 3.92% of reference with a coverageData >= 1X There is a 2.61% of reference with a coverageData >= 2X There is a 2.12% of reference with a coverageData >= 3X There is a 1.88% of reference with a coverageData >= 4X There is a 1.71% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.49% of reference with a coverageData >= 7X There is a 1.4% of reference with a coverageData >= 8X There is a 1.33% of reference with a coverageData >= 9X There is a 1.27% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1.16% of reference with a coverageData >= 12X There is a 1.11% of reference with a coverageData >= 13X There is a 1.07% of reference with a coverageData >= 14X There is a 1.03% of reference with a coverageData >= 15X There is a 0.99% of reference with a coverageData >= 16X There is a 0.96% of reference with a coverageData >= 17X There is a 0.93% of reference with a coverageData >= 18X There is a 0.9% of reference with a coverageData >= 19X There is a 0.87% of reference with a coverageData >= 20X There is a 0.84% of reference with a coverageData >= 21X There is a 0.82% of reference with a coverageData >= 22X There is a 0.8% of reference with a coverageData >= 23X There is a 0.78% of reference with a coverageData >= 24X There is a 0.76% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.72% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.68% of reference with a coverageData >= 29X There is a 0.67% of reference with a coverageData >= 30X There is a 0.65% of reference with a coverageData >= 31X There is a 0.64% of reference with a coverageData >= 32X There is a 0.62% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.6% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.57% of reference with a coverageData >= 37X There is a 0.56% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.52% of reference with a coverageData >= 42X There is a 0.51% of reference with a coverageData >= 43X There is a 0.5% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.48% of reference with a coverageData >= 47X There is a 0.47% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.45% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197417574 0.7920444619473987 35.95659739482423 chr2 243199373 260016316 1.0691487925834413 26.201056331643624 chr3 198022430 282712419 1.4276787685112238 42.47963866493904 chr4 191154276 939566903 4.915228278754277 73.59697436712955 chr5 180915260 142528608 0.7878197118363592 12.401657108624665 chr6 171115067 75201677 0.43948015986225225 9.742961802111093 chr7 159138663 199461899 1.2533842828628012 55.44038105165741 chr8 146364022 70842216 0.4840138651013567 17.70771540492984 chr9 141213431 102643241 0.7268659947792077 17.45797967296409 chr10 135534747 273056833 2.0146629483876928 46.264609478308536 chr11 135006516 147060770 1.0892864608105286 18.747046101497276 chr12 133851895 256336628 1.9150765702644703 20.749033821872732 chr13 115169878 50956883 0.4424497436734282 19.153611517750765 chr14 107349540 65965924 0.6144965688721162 11.232582077835337 chr15 102531392 302591949 2.951212727122636 46.54841314401526 chr16 90354753 61065296 0.6758393329900421 21.03333082436118 chr17 81195210 189137611 2.3294183363772323 47.453688431216136 chr18 78077248 25235164 0.3232076519910128 8.36583377013136 chr19 59128983 121556943 2.0557928926327045 29.295108207536785 chr20 63025520 28102609 0.44589253686443203 16.7713828779971 chr21 48129895 23487766 0.48800783795601466 20.312864602589 chr22 51304566 144685952 2.8201379191084084 28.365417109130533 chrMT 16571 2115372 127.65506004465632 63.19467740651618 chrX 155270560 50287183 0.3238681112504521 13.074641388792537 chrY 59373566 13988159 0.23559573632481498 21.048085075731503