BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472558.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,104,146 number of mapped reads = 9,909,638 (98.07%) number of supplementary alignments = 43,424 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,974,341 number of mapped paired reads (second in pair) = 4,935,297 number of mapped paired reads (both in pair) = 9,819,640 number of mapped paired reads (singletons) = 89,998 number of mapped bases = 970,043,538 bp number of sequenced bases = 969,912,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,362,377 duplication rate = 42.77% >>>>>>> Insert size mean insert size = 37,306.9531 std insert size = 1,882,786.0954 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 54.9369 >>>>>>> ACTG content number of A's = 273,709,583 bp (28.22%) number of C's = 213,302,033 bp (21.99%) number of T's = 271,010,840 bp (27.94%) number of G's = 211,740,661 bp (21.83%) number of N's = 149,623 bp (0.02%) GC percentage = 43.82% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 6,169,426 number of insertions = 54,863 mapped reads with insertion percentage = 0.55% number of deletions = 52,996 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.3134X std coverageData = 10.2151X There is a 3.44% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 107493864 0.43126818929771094 14.771015819009344 chr2 243199373 56495243 0.2323001178132149 8.232347973058152 chr3 198022430 110362743 0.5573244556184873 16.85254572716804 chr4 191154276 42429247 0.22196336847834888 8.085138321610053 chr5 180915260 58986293 0.3260437676733295 10.444503888284155 chr6 171115067 63196291 0.36932043511983664 10.06814904987238 chr7 159138663 40575471 0.25496928423987075 7.923500688250481 chr8 146364022 41677629 0.28475323669364594 8.560851987382996 chr9 141213431 62933920 0.445665256869228 11.268394681306766 chr10 135534747 27641128 0.2039412668103479 7.052879378698709 chr11 135006516 56251640 0.41665870408803085 13.695169639177399 chr12 133851895 48591532 0.3630246101484032 9.824318086328763 chr13 115169878 22853228 0.19843060005672664 6.74342065080234 chr14 107349540 25466821 0.23723269796964197 8.101184610840413 chr15 102531392 21421469 0.20892595508700398 7.051033708941408 chr16 90354753 29691352 0.32860863445667327 8.661244315184707 chr17 81195210 34609216 0.4262470162956657 8.530289263614208 chr18 78077248 19037381 0.24382751041635073 9.06346418067905 chr19 59128983 15021429 0.25404511016196574 6.022142588530535 chr20 63025520 18822333 0.29864621505701183 8.261335002495844 chr21 48129895 4601683 0.0956096621444946 3.2727054014198416 chr22 51304566 7624483 0.1486121722577285 3.371178056579568 chrMT 16571 1383 0.08345905497555971 0.31166024113773105 chrX 155270560 52231763 0.3363919277421296 10.912205319589773 chrY 59373566 2025996 0.034122862015732724 1.663360628152779