BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617704.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 53,893,928 number of mapped reads = 53,030,430 (98.4%) number of supplementary alignments = 973,007 (1.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,797,710 number of mapped paired reads (second in pair) = 26,232,720 number of mapped paired reads (both in pair) = 52,395,224 number of mapped paired reads (singletons) = 635,206 number of mapped bases = 7,062,781,499 bp number of sequenced bases = 7,057,565,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,407,939 duplication rate = 28.44% >>>>>>> Insert size mean insert size = 107,826.4022 std insert size = 3,148,400.3804 median insert size = 267 >>>>>>> Mapping quality mean mapping quality = 53.6616 >>>>>>> ACTG content number of A's = 2,037,329,072 bp (28.87%) number of C's = 1,334,688,118 bp (18.91%) number of T's = 2,116,618,267 bp (29.99%) number of G's = 1,568,630,432 bp (22.23%) number of N's = 299,582 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 77,748,132 number of insertions = 1,181,974 mapped reads with insertion percentage = 2.1% number of deletions = 2,765,432 mapped reads with deletion percentage = 5.01% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 2.2815X std coverageData = 22.4232X There is a 42.43% of reference with a coverageData >= 1X There is a 31.84% of reference with a coverageData >= 2X There is a 24.34% of reference with a coverageData >= 3X There is a 19.32% of reference with a coverageData >= 4X There is a 15.46% of reference with a coverageData >= 5X There is a 12.6% of reference with a coverageData >= 6X There is a 10.33% of reference with a coverageData >= 7X There is a 8.57% of reference with a coverageData >= 8X There is a 7.15% of reference with a coverageData >= 9X There is a 6.01% of reference with a coverageData >= 10X There is a 5.08% of reference with a coverageData >= 11X There is a 4.32% of reference with a coverageData >= 12X There is a 3.69% of reference with a coverageData >= 13X There is a 3.16% of reference with a coverageData >= 14X There is a 2.72% of reference with a coverageData >= 15X There is a 2.35% of reference with a coverageData >= 16X There is a 2.04% of reference with a coverageData >= 17X There is a 1.78% of reference with a coverageData >= 18X There is a 1.55% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.2% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.83% of reference with a coverageData >= 24X There is a 0.73% of reference with a coverageData >= 25X There is a 0.65% of reference with a coverageData >= 26X There is a 0.58% of reference with a coverageData >= 27X There is a 0.52% of reference with a coverageData >= 28X There is a 0.47% of reference with a coverageData >= 29X There is a 0.42% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 659095644 2.6443089343396258 20.811450000434856 chr2 243199373 481104834 1.9782322136167678 25.838571466568443 chr3 198022430 474669324 2.3970482737738346 4.869111552041725 chr4 191154276 355246448 1.858427943301671 14.108182283966144 chr5 180915260 394786194 2.1821608304351994 4.993324595134205 chr6 171115067 415049776 2.4255594979254513 14.49714651526064 chr7 159138663 432194094 2.7158333861331987 33.789159081657175 chr8 146364022 409958279 2.8009498058204496 8.10350452040854 chr9 141213431 302945642 2.14530331750101 33.43664518441753 chr10 135534747 344759900 2.543701210435727 61.467396266692546 chr11 135006516 304095153 2.2524479707335017 21.13381471557059 chr12 133851895 423828115 3.166396075303977 13.496404055514239 chr13 115169878 245787290 2.1341282483602177 4.652610345437859 chr14 107349540 208236813 1.9398016330577663 4.7435814928445 chr15 102531392 132853195 1.2957318964322653 5.235819176841872 chr16 90354753 227248126 2.515065543923295 29.209111448167068 chr17 81195210 167144367 2.0585495991697047 18.75088872382381 chr18 78077248 212776116 2.725199996803166 29.720321510075262 chr19 59128983 119112364 2.014449732713989 13.220657933599298 chr20 63025520 156872841 2.48903683777619 6.383942456157357 chr21 48129895 69446972 1.4429071993612286 7.4085606629048595 chr22 51304566 59805219 1.1656899894640957 4.136768312122878 chrMT 16571 974142 58.785951360811055 31.988027804242737 chrX 155270560 373065498 2.402680186121567 7.029025950674059 chrY 59373566 91725153 1.5448819934446922 29.01757915135124