BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231737.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 = 1,670,389 number of mapped reads = 526,106 (31.5%) number of supplementary alignments = 3,702 (0.22%) number of secondary alignments = 0 number of mapped bases = 32,568,637 bp number of sequenced bases = 32,548,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,495 duplication rate = 7.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.792 >>>>>>> ACTG content number of A's = 8,982,845 bp (27.6%) number of C's = 5,392,501 bp (16.57%) number of T's = 10,993,700 bp (33.78%) number of G's = 7,178,338 bp (22.05%) number of N's = 835 bp (0%) GC percentage = 38.62% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 328,067 number of insertions = 3,545 mapped reads with insertion percentage = 0.66% number of deletions = 11,675 mapped reads with deletion percentage = 2.18% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 0.236X There is a 0.79% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.05% 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% 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 3114373 0.012494945799954497 0.21453244350859443 chr2 243199373 2065052 0.008491189654506223 0.1671076512049893 chr3 198022430 3386068 0.017099416465094382 0.17459371601953974 chr4 191154276 1646075 0.008611238181247904 0.13097529634015168 chr5 180915260 3103428 0.01715404217422013 0.17383047962898107 chr6 171115067 1341138 0.007837638283483243 0.12767205330894466 chr7 159138663 1281332 0.008051670008060832 0.1453101209305232 chr8 146364022 1092757 0.007466021943562059 0.7960680635311156 chr9 141213431 1393213 0.009866009133366358 0.14513912318081362 chr10 135534747 1863487 0.013749145818673347 0.16858843348542274 chr11 135006516 1421812 0.010531432423602428 0.1450143256423645 chr12 133851895 1239785 0.009262364197383981 0.13822288739244853 chr13 115169878 2088398 0.01813319625119339 0.18763451424500613 chr14 107349540 651486 0.006068828986132591 0.103408427565605 chr15 102531392 616178 0.0060096521463397275 0.12711116544139048 chr16 90354753 1636604 0.018113092512133812 0.17853243148679146 chr17 81195210 775038 0.009545366038218265 0.12671871749501906 chr18 78077248 474187 0.006073305759957113 0.35369305373008886 chr19 59128983 729975 0.012345468549662016 0.17999663286757656 chr20 63025520 373992 0.005933977220656013 0.10595583732741426 chr21 48129895 273788 0.00568852269467864 0.10447930884380657 chr22 51304566 365398 0.007122134119602532 0.10443927952864897 chrMT 16571 10390 0.6269989741113995 1.0517296299727337 chrX 155270560 1512345 0.00974006276527888 0.1477664821706766 chrY 59373566 112338 0.0018920541171470145 0.056619630427780954