BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975202.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 51,961,912 number of mapped reads = 51,829,191 (99.74%) number of supplementary alignments = 115,719 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,910,878 number of mapped paired reads (second in pair) = 25,918,313 number of mapped paired reads (both in pair) = 51,747,190 number of mapped paired reads (singletons) = 82,001 number of mapped bases = 4,901,508,857 bp number of sequenced bases = 4,899,713,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,923,264 duplication rate = 47.2% >>>>>>> Insert size mean insert size = 159,737.3068 std insert size = 3,942,628.0227 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.7902 >>>>>>> ACTG content number of A's = 1,324,892,902 bp (27.04%) number of C's = 1,082,980,533 bp (22.1%) number of T's = 1,347,597,163 bp (27.5%) number of G's = 1,143,994,389 bp (23.35%) number of N's = 248,460 bp (0.01%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 29,576,419 number of insertions = 573,495 mapped reads with insertion percentage = 1.09% number of deletions = 1,158,442 mapped reads with deletion percentage = 2.2% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 1.5833X std coverageData = 28.1355X There is a 9.84% of reference with a coverageData >= 1X There is a 4.93% of reference with a coverageData >= 2X There is a 3.02% of reference with a coverageData >= 3X There is a 2.28% of reference with a coverageData >= 4X There is a 1.91% of reference with a coverageData >= 5X There is a 1.7% of reference with a coverageData >= 6X There is a 1.56% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.39% of reference with a coverageData >= 9X There is a 1.32% of reference with a coverageData >= 10X There is a 1.27% of reference with a coverageData >= 11X There is a 1.22% of reference with a coverageData >= 12X There is a 1.18% of reference with a coverageData >= 13X There is a 1.14% of reference with a coverageData >= 14X There is a 1.11% of reference with a coverageData >= 15X There is a 1.08% of reference with a coverageData >= 16X There is a 1.05% of reference with a coverageData >= 17X There is a 1.02% of reference with a coverageData >= 18X There is a 1% of reference with a coverageData >= 19X There is a 0.97% of reference with a coverageData >= 20X There is a 0.95% of reference with a coverageData >= 21X There is a 0.93% of reference with a coverageData >= 22X There is a 0.91% of reference with a coverageData >= 23X There is a 0.89% of reference with a coverageData >= 24X There is a 0.87% of reference with a coverageData >= 25X There is a 0.85% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.81% of reference with a coverageData >= 29X There is a 0.79% of reference with a coverageData >= 30X There is a 0.78% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.75% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.73% of reference with a coverageData >= 35X There is a 0.72% of reference with a coverageData >= 36X There is a 0.7% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.68% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.66% of reference with a coverageData >= 41X There is a 0.65% of reference with a coverageData >= 42X There is a 0.64% of reference with a coverageData >= 43X There is a 0.63% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.6% of reference with a coverageData >= 48X There is a 0.59% of reference with a coverageData >= 49X There is a 0.58% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 610566933 2.449610478603381 36.51860644790962 chr2 243199373 309181077 1.271307048147694 21.621486480658305 chr3 198022430 412050611 2.0808279698415983 32.904852529593946 chr4 191154276 182877025 0.9566985830858421 18.84532354818847 chr5 180915260 318026656 1.7578763449805175 29.758555441562645 chr6 171115067 280365286 1.638460545382599 30.643853540017545 chr7 159138663 193288202 1.2145898322647086 23.26720683234381 chr8 146364022 196257121 1.3408836291749349 23.775383664795257 chr9 141213431 165916866 1.1749368656016863 24.512821504234076 chr10 135534747 182503083 1.346540920609827 22.204254472373467 chr11 135006516 235020182 1.7408062141237686 29.20317990376509 chr12 133851895 234897720 1.7549076910715384 28.186405105290614 chr13 115169878 77970228 0.6770019153792973 16.036903333672935 chr14 107349540 154439022 1.4386556477093428 24.134869638808752 chr15 102531392 140041124 1.3658365625232125 24.717993129801318 chr16 90354753 134634619 1.4900668147474212 24.405662256823433 chr17 81195210 178538117 2.198874995212156 33.61117173274942 chr18 78077248 100206926 1.283433119978819 23.68033122040424 chr19 59128983 223377378 3.7777984106373013 57.63166334092976 chr20 63025520 110800830 1.7580311911746227 28.89854633104714 chr21 48129895 42668919 0.8865367148629766 20.541854417292942 chr22 51304566 65650491 1.2796227727567173 23.95757522358199 chrMT 16571 596569 36.00078450304749 42.32052600404516 chrX 155270560 346717136 2.2329869615978715 37.135924232535515 chrY 59373566 4916736 0.08281018525988484 4.297686642430612