BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472649.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 = 9,867,382 number of mapped reads = 9,791,994 (99.24%) number of supplementary alignments = 47,526 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,902,517 number of mapped paired reads (second in pair) = 4,889,477 number of mapped paired reads (both in pair) = 9,743,470 number of mapped paired reads (singletons) = 48,524 number of mapped bases = 960,289,250 bp number of sequenced bases = 960,140,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,691,019 duplication rate = 43.59% >>>>>>> Insert size mean insert size = 17,277.9227 std insert size = 1,320,763.8896 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 54.7605 >>>>>>> ACTG content number of A's = 255,640,131 bp (26.63%) number of C's = 226,073,631 bp (23.55%) number of T's = 256,163,400 bp (26.68%) number of G's = 222,131,411 bp (23.14%) number of N's = 131,893 bp (0.01%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 6,896,509 number of insertions = 52,296 mapped reads with insertion percentage = 0.53% number of deletions = 49,162 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.3102X std coverageData = 19.6958X There is a 2.22% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133368100 0.5350762997697807 29.24382391453282 chr2 243199373 57133407 0.23492415418357185 10.544279580804634 chr3 198022430 82174776 0.41497711143126564 24.61740930599455 chr4 191154276 26868878 0.14056121872994357 11.451012872039584 chr5 180915260 49425293 0.2731958210711468 14.754472473637732 chr6 171115067 95952867 0.5607505445443913 25.81565775949883 chr7 159138663 33228649 0.2088031178193322 8.922269536105413 chr8 146364022 84263205 0.575709821639091 34.98280709817339 chr9 141213431 52066451 0.3687074992179745 32.93467597271119 chr10 135534747 18259313 0.13472053037439913 12.186237774119173 chr11 135006516 31825023 0.2357295332323071 13.078598097172655 chr12 133851895 55210228 0.41247251673201935 25.683904797019565 chr13 115169878 16923450 0.14694337003639094 10.184847116136567 chr14 107349540 12119569 0.1128981922046429 4.4768327145380375 chr15 102531392 15141866 0.1476802928804478 9.504429445660294 chr16 90354753 30424203 0.33671945293237643 12.366906435399624 chr17 81195210 52362843 0.6449006413063036 24.329831329445184 chr18 78077248 16989186 0.21759458017782593 17.30215954073664 chr19 59128983 21144660 0.35760229463104415 14.711775644218264 chr20 63025520 24275295 0.3851661200097992 18.39619987221525 chr21 48129895 5113341 0.10624043538844205 6.518138530312408 chr22 51304566 12865149 0.2507603124447052 13.44540186385643 chrMT 16571 184 0.01110373544143383 0.10478760661776981 chrX 155270560 32293765 0.20798382513723143 14.253306777928378 chrY 59373566 859549 0.014476964378390208 0.825940622518343