BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472748.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 = 10,567,986 number of mapped reads = 10,437,460 (98.76%) number of supplementary alignments = 37,109 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,242,321 number of mapped paired reads (second in pair) = 5,195,139 number of mapped paired reads (both in pair) = 10,363,112 number of mapped paired reads (singletons) = 74,348 number of mapped bases = 1,027,205,189 bp number of sequenced bases = 1,027,064,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,027,464 duplication rate = 44.54% >>>>>>> Insert size mean insert size = 28,123.817 std insert size = 1,625,563.3225 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 55.2581 >>>>>>> ACTG content number of A's = 287,349,468 bp (27.98%) number of C's = 227,851,069 bp (22.18%) number of T's = 284,708,458 bp (27.72%) number of G's = 226,959,125 bp (22.1%) number of N's = 196,811 bp (0.02%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 6,644,339 number of insertions = 59,157 mapped reads with insertion percentage = 0.56% number of deletions = 57,433 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.3318X std coverageData = 12.2434X There is a 3.12% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.51% 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 0.23% 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 0.2% 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 103072663 0.4135302154372566 14.840479548319447 chr2 243199373 85224008 0.3504285679223359 17.141114458536016 chr3 198022430 133488674 0.6741088572643008 16.653489267662334 chr4 191154276 40527102 0.21201253169978787 8.439066857290145 chr5 180915260 53675601 0.2966891847597599 9.299346208595022 chr6 171115067 51277430 0.2996663642717096 8.508756296432196 chr7 159138663 49355835 0.3101435821413179 10.630259825375743 chr8 146364022 38816185 0.26520304969482184 8.604343171319119 chr9 141213431 63094791 0.44680446153878944 17.598353773992436 chr10 135534747 28994161 0.21392419022997844 8.573399923273971 chr11 135006516 50901051 0.3770266244038177 14.469637778435919 chr12 133851895 54880549 0.41000950341420267 15.766812048521833 chr13 115169878 32536195 0.2825061167469501 12.330387827254071 chr14 107349540 17579430 0.16375878275770908 7.131546137416549 chr15 102531392 26437263 0.2578455484150649 10.351722636629447 chr16 90354753 38138481 0.42209711978295156 12.964280714410311 chr17 81195210 34515820 0.4250967513970344 9.70028660596558 chr18 78077248 16712573 0.21405176832052278 8.988936495393546 chr19 59128983 16543008 0.27977832799863983 7.194003788877892 chr20 63025520 24324533 0.3859473591015195 10.840366715180505 chr21 48129895 6252379 0.12990635030473263 6.315615670213778 chr22 51304566 10473397 0.20414161577743392 5.777353838750108 chrMT 16571 2547 0.15370225092028242 0.5467422275241208 chrX 155270560 49288631 0.31743706598340343 11.295959947159615 chrY 59373566 1092882 0.0184068782393835 0.5621656257172866