BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365352.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 = 570,379,364 number of mapped reads = 551,413,701 (96.67%) number of supplementary alignments = 2,357,407 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 276,236,200 number of mapped paired reads (second in pair) = 275,177,501 number of mapped paired reads (both in pair) = 548,996,588 number of mapped paired reads (singletons) = 2,417,113 number of mapped bases = 57,300,882,370 bp number of sequenced bases = 57,282,062,072 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,912,468 duplication rate = 32.82% >>>>>>> Insert size mean insert size = 62,618.5877 std insert size = 2,438,586.207 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 53.8537 >>>>>>> ACTG content number of A's = 17,208,381,329 bp (30.04%) number of C's = 11,258,796,638 bp (19.66%) number of T's = 16,727,985,396 bp (29.2%) number of G's = 12,080,770,398 bp (21.09%) number of N's = 6,128,311 bp (0.01%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 286,949,886 number of insertions = 17,079,760 mapped reads with insertion percentage = 3.03% number of deletions = 8,962,287 mapped reads with deletion percentage = 1.58% homopolymer indels = 50.6% >>>>>>> Coverage mean coverageData = 18.5099X std coverageData = 127.9371X There is a 83.89% of reference with a coverageData >= 1X There is a 81.78% of reference with a coverageData >= 2X There is a 78.88% of reference with a coverageData >= 3X There is a 76.57% of reference with a coverageData >= 4X There is a 73.75% of reference with a coverageData >= 5X There is a 71.28% of reference with a coverageData >= 6X There is a 68.46% of reference with a coverageData >= 7X There is a 65.91% of reference with a coverageData >= 8X There is a 63.13% of reference with a coverageData >= 9X There is a 60.57% of reference with a coverageData >= 10X There is a 57.86% of reference with a coverageData >= 11X There is a 55.34% of reference with a coverageData >= 12X There is a 52.74% of reference with a coverageData >= 13X There is a 50.31% of reference with a coverageData >= 14X There is a 47.84% of reference with a coverageData >= 15X There is a 45.54% of reference with a coverageData >= 16X There is a 43.22% of reference with a coverageData >= 17X There is a 41.06% of reference with a coverageData >= 18X There is a 38.91% of reference with a coverageData >= 19X There is a 36.89% of reference with a coverageData >= 20X There is a 34.91% of reference with a coverageData >= 21X There is a 33.06% of reference with a coverageData >= 22X There is a 31.24% of reference with a coverageData >= 23X There is a 29.54% of reference with a coverageData >= 24X There is a 27.88% of reference with a coverageData >= 25X There is a 26.33% of reference with a coverageData >= 26X There is a 24.82% of reference with a coverageData >= 27X There is a 23.41% of reference with a coverageData >= 28X There is a 22.04% of reference with a coverageData >= 29X There is a 20.77% of reference with a coverageData >= 30X There is a 19.54% of reference with a coverageData >= 31X There is a 18.39% of reference with a coverageData >= 32X There is a 17.29% of reference with a coverageData >= 33X There is a 16.26% of reference with a coverageData >= 34X There is a 15.27% of reference with a coverageData >= 35X There is a 14.35% of reference with a coverageData >= 36X There is a 13.47% of reference with a coverageData >= 37X There is a 12.65% of reference with a coverageData >= 38X There is a 11.86% of reference with a coverageData >= 39X There is a 11.13% of reference with a coverageData >= 40X There is a 10.44% of reference with a coverageData >= 41X There is a 9.79% of reference with a coverageData >= 42X There is a 9.18% of reference with a coverageData >= 43X There is a 8.61% of reference with a coverageData >= 44X There is a 8.07% of reference with a coverageData >= 45X There is a 7.56% of reference with a coverageData >= 46X There is a 7.09% of reference with a coverageData >= 47X There is a 6.64% of reference with a coverageData >= 48X There is a 6.22% of reference with a coverageData >= 49X There is a 5.83% of reference with a coverageData >= 50X There is a 5.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4688955324 18.812211200067583 327.2030249724352 chr2 243199373 5001895052 20.567055705361543 81.98191994544204 chr3 198022430 3933441069 19.86361377849974 25.592019102914097 chr4 191154276 3990375341 20.875156049347282 93.30058620104043 chr5 180915260 3588296085 19.834126126231695 21.037630508325428 chr6 171115067 3448884090 20.155350142252523 57.85767121131207 chr7 159138663 3178517859 19.973259791682427 98.10434547816378 chr8 146364022 2950557150 20.159033003342856 35.89629270194587 chr9 141213431 2418297928 17.125126915158656 94.0804035175354 chr10 135534747 2863873192 21.130176987012785 248.4615412273814 chr11 135006516 2656109278 19.67393394552897 79.61060729824577 chr12 133851895 2611592945 19.51106441190093 34.4978733907436 chr13 115169878 1937872479 16.8262093583185 18.203498100467282 chr14 107349540 1767603865 16.46587274617106 19.972813952840053 chr15 102531392 1605100352 15.654721160910407 23.307381049794987 chr16 90354753 1603890612 17.751037535346924 45.80948869737691 chr17 81195210 1514087786 18.647501324277627 92.61849124705688 chr18 78077248 1609762974 20.61756805260349 152.8815799332718 chr19 59128983 1040368542 17.594899983312754 162.7699067306176 chr20 63025520 1172766375 18.60780164923669 32.11193541884294 chr21 48129895 817986497 16.995393341290274 66.04038284583498 chr22 51304566 656210101 12.79048147488471 59.14811812139441 chrMT 16571 78631224 4745.110373544143 782.0457024235671 chrX 155270560 1601395630 10.313581853507838 37.70518021414836 chrY 59373566 564410620 9.50609266083159 186.14888540074662