BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365335.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 108,727,676 number of mapped reads = 106,299,756 (97.77%) number of supplementary alignments = 872,770 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,373,048 number of mapped paired reads (second in pair) = 52,926,708 number of mapped paired reads (both in pair) = 105,691,026 number of mapped paired reads (singletons) = 608,730 number of mapped bases = 13,911,567,962 bp number of sequenced bases = 13,906,492,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,965,837 duplication rate = 31.05% >>>>>>> Insert size mean insert size = 92,442.947 std insert size = 3,006,800.643 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 54.348 >>>>>>> ACTG content number of A's = 4,140,589,689 bp (29.77%) number of C's = 2,765,422,333 bp (19.89%) number of T's = 4,089,662,427 bp (29.41%) number of G's = 2,910,320,362 bp (20.93%) number of N's = 497,299 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 90,785,366 number of insertions = 4,326,675 mapped reads with insertion percentage = 3.95% number of deletions = 2,079,453 mapped reads with deletion percentage = 1.89% homopolymer indels = 50.98% >>>>>>> Coverage mean coverageData = 4.4938X std coverageData = 29.8353X There is a 75.25% of reference with a coverageData >= 1X There is a 66.18% of reference with a coverageData >= 2X There is a 54.75% of reference with a coverageData >= 3X There is a 46.26% of reference with a coverageData >= 4X There is a 37.63% of reference with a coverageData >= 5X There is a 31.05% of reference with a coverageData >= 6X There is a 24.97% of reference with a coverageData >= 7X There is a 20.29% of reference with a coverageData >= 8X There is a 16.19% of reference with a coverageData >= 9X There is a 13.03% of reference with a coverageData >= 10X There is a 10.35% of reference with a coverageData >= 11X There is a 8.28% of reference with a coverageData >= 12X There is a 6.56% of reference with a coverageData >= 13X There is a 5.23% of reference with a coverageData >= 14X There is a 4.14% of reference with a coverageData >= 15X There is a 3.3% of reference with a coverageData >= 16X There is a 2.62% of reference with a coverageData >= 17X There is a 2.09% of reference with a coverageData >= 18X There is a 1.67% of reference with a coverageData >= 19X There is a 1.34% of reference with a coverageData >= 20X There is a 1.07% of reference with a coverageData >= 21X There is a 0.87% of reference with a coverageData >= 22X There is a 0.7% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1182989415 4.746184423749138 74.61135034007407 chr2 243199373 1225228445 5.037958897204887 20.124244108431323 chr3 198022430 957938147 4.837523441157651 5.49444255006199 chr4 191154276 916672311 4.795458046672207 20.289957852099867 chr5 180915260 863093346 4.7707050582687165 5.597387309543335 chr6 171115067 843717291 4.930701344961049 16.936254467210226 chr7 159138663 766447490 4.816224263490262 17.587064720814354 chr8 146364022 701014268 4.7895258576592 10.574116029766998 chr9 141213431 602880261 4.2692841377106685 27.28003613892988 chr10 135534747 710235592 5.240247299830796 54.811685114729514 chr11 135006516 646791249 4.790815052215702 21.519396550605936 chr12 133851895 640278170 4.783482295861407 27.35644011385855 chr13 115169878 445283148 3.8663160518412636 4.604350888234348 chr14 107349540 439160400 4.090938815387565 5.033810381009108 chr15 102531392 414462184 4.042295495217699 13.077232343734769 chr16 90354753 388990324 4.305145120589284 11.345403540896486 chr17 81195210 421238495 5.18797223383005 22.51111485489071 chr18 78077248 363721282 4.658479791705774 33.7964326705797 chr19 59128983 253132074 4.281015183366168 38.05613915842214 chr20 63025520 286510319 4.545941374224283 8.744429537980121 chr21 48129895 192490803 3.9994020971788946 15.654852797462455 chr22 51304566 175662593 3.42391733710407 13.185270396425514 chrMT 16571 16037632 967.8131675819202 203.6754666501856 chrX 155270560 351951495 2.2666981751080177 8.238953008107197 chrY 59373566 105641228 1.779263654131874 37.938639918048366