BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617491.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,603,200 (95.64%) number of supplementary alignments = 158,418 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,416,224 number of mapped paired reads (second in pair) = 15,186,976 number of mapped paired reads (both in pair) = 30,091,210 number of mapped paired reads (singletons) = 511,990 number of mapped bases = 2,981,394,428 bp number of sequenced bases = 2,979,618,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,322,665 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 37,622.9397 std insert size = 1,796,888.8096 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.7374 >>>>>>> ACTG content number of A's = 878,120,378 bp (29.47%) number of C's = 602,286,466 bp (20.21%) number of T's = 878,470,983 bp (29.48%) number of G's = 617,659,783 bp (20.73%) number of N's = 3,080,532 bp (0.1%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 35,566,700 number of insertions = 445,520 mapped reads with insertion percentage = 1.43% number of deletions = 1,039,587 mapped reads with deletion percentage = 3.33% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.9631X std coverageData = 9.6643X There is a 38.27% of reference with a coverageData >= 1X There is a 20.68% of reference with a coverageData >= 2X There is a 11.69% of reference with a coverageData >= 3X There is a 6.96% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.76% of reference with a coverageData >= 6X There is a 1.83% of reference with a coverageData >= 7X There is a 1.25% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192305435 0.7715344267888504 9.449580670805585 chr2 243199373 308053950 1.266672467942588 11.426117055262486 chr3 198022430 245896090 1.2417587744984242 2.242535192194219 chr4 191154276 153755224 0.8043514757681905 6.068132701410423 chr5 180915260 190903444 1.0552091846757428 2.095674064190867 chr6 171115067 140415143 0.8205890075127049 5.4120767515415436 chr7 159138663 229989074 1.4452118024895055 13.190425665073427 chr8 146364022 132355719 0.9042913496870153 3.8773202369915762 chr9 141213431 123352865 0.8735207701312774 18.203025810049407 chr10 135534747 126229569 0.9313447052806318 18.59327969723429 chr11 135006516 168424982 1.2475322450362323 12.669581450895839 chr12 133851895 130269445 0.9732357169840591 1.9973987597033465 chr13 115169878 126516630 1.098521872186059 2.1296771783045285 chr14 107349540 86763932 0.8082375760529574 2.2376855890292147 chr15 102531392 67524242 0.6585713963582978 1.4958046386432355 chr16 90354753 80385092 0.8896609124702051 14.696411903957182 chr17 81195210 83435998 1.0275975393129717 13.50736006765709 chr18 78077248 53198172 0.6813530620341537 16.98873300922352 chr19 59128983 35806356 0.605563535567659 5.813522188361748 chr20 63025520 88304868 1.4010970159389402 2.830033830119115 chr21 48129895 42986750 0.893140323701101 3.802051980125479 chr22 51304566 22323157 0.43511053187741616 1.2499318811539624 chrMT 16571 2137173 128.97067165530143 97.56802697406947 chrX 155270560 139834411 0.9005854747996014 4.10065869018807 chrY 59373566 10226707 0.17224343574041012 13.53322863439476