BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975196.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 55,135,976 number of mapped reads = 54,991,588 (99.74%) number of supplementary alignments = 146,836 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,491,326 number of mapped paired reads (second in pair) = 27,500,262 number of mapped paired reads (both in pair) = 54,906,892 number of mapped paired reads (singletons) = 84,696 number of mapped bases = 5,181,593,740 bp number of sequenced bases = 5,179,499,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,158,637 duplication rate = 48.09% >>>>>>> Insert size mean insert size = 178,720.3598 std insert size = 4,155,018.9032 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 55.7093 >>>>>>> ACTG content number of A's = 1,394,638,988 bp (26.93%) number of C's = 1,159,799,777 bp (22.39%) number of T's = 1,398,774,717 bp (27.01%) number of G's = 1,226,018,140 bp (23.67%) number of N's = 267,817 bp (0.01%) GC percentage = 46.06% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 37,883,254 number of insertions = 588,636 mapped reads with insertion percentage = 1.06% number of deletions = 1,461,912 mapped reads with deletion percentage = 2.61% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 1.6738X std coverageData = 29.3006X There is a 9.93% of reference with a coverageData >= 1X There is a 4.92% of reference with a coverageData >= 2X There is a 3.02% of reference with a coverageData >= 3X There is a 2.3% of reference with a coverageData >= 4X There is a 1.93% of reference with a coverageData >= 5X There is a 1.73% of reference with a coverageData >= 6X There is a 1.6% of reference with a coverageData >= 7X There is a 1.5% of reference with a coverageData >= 8X There is a 1.43% of reference with a coverageData >= 9X There is a 1.37% of reference with a coverageData >= 10X There is a 1.31% of reference with a coverageData >= 11X There is a 1.27% of reference with a coverageData >= 12X There is a 1.23% of reference with a coverageData >= 13X There is a 1.19% of reference with a coverageData >= 14X There is a 1.15% of reference with a coverageData >= 15X There is a 1.12% of reference with a coverageData >= 16X There is a 1.09% of reference with a coverageData >= 17X There is a 1.07% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 1.02% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.97% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.9% of reference with a coverageData >= 26X There is a 0.88% of reference with a coverageData >= 27X There is a 0.86% of reference with a coverageData >= 28X There is a 0.85% of reference with a coverageData >= 29X There is a 0.83% of reference with a coverageData >= 30X There is a 0.82% of reference with a coverageData >= 31X There is a 0.8% of reference with a coverageData >= 32X There is a 0.79% of reference with a coverageData >= 33X There is a 0.78% of reference with a coverageData >= 34X There is a 0.76% of reference with a coverageData >= 35X There is a 0.75% of reference with a coverageData >= 36X There is a 0.74% of reference with a coverageData >= 37X There is a 0.73% of reference with a coverageData >= 38X There is a 0.72% of reference with a coverageData >= 39X There is a 0.71% of reference with a coverageData >= 40X There is a 0.7% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.66% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.63% of reference with a coverageData >= 49X There is a 0.62% of reference with a coverageData >= 50X There is a 0.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 593423727 2.380831488480023 37.25097186774531 chr2 243199373 331776977 1.3642180607102141 23.10404484819787 chr3 198022430 430448569 2.1737364247070396 31.671076826860574 chr4 191154276 192116118 1.0050317576992105 18.875989993619232 chr5 180915260 373985781 2.067187593793912 33.1769047223617 chr6 171115067 305539641 1.7855799980489153 32.99881564571637 chr7 159138663 212888647 1.3377556590380555 24.156678058323518 chr8 146364022 173850215 1.1877933704226848 20.984299405369736 chr9 141213431 191714998 1.3576258054377277 24.43811289251696 chr10 135534747 192268658 1.4185931080831988 24.64862147752567 chr11 135006516 285682997 2.116068212589087 32.11860593112266 chr12 133851895 245224770 1.8320605023933356 28.155483661989564 chr13 115169878 70298165 0.6103867280297024 17.734540782938446 chr14 107349540 175416254 1.6340661916203834 26.742814350804842 chr15 102531392 152032001 1.4827849113762155 24.35650601935035 chr16 90354753 143929408 1.5929367655954967 26.345757144817966 chr17 81195210 184164770 2.268172839259853 36.27885736039921 chr18 78077248 83113346 1.06450147935542 25.246692616510284 chr19 59128983 254194288 4.2989795376659865 59.39913360708888 chr20 63025520 112148268 1.7794104356457512 32.3506075309373 chr21 48129895 41098489 0.8539077220093665 16.180795209572427 chr22 51304566 77631856 1.5131568601515897 27.788633109889474 chrMT 16571 455502 27.487900549152133 34.15173849670068 chrX 155270560 356152560 2.293754591984469 39.223779210943306 chrY 59373566 2037735 0.034320576264528224 2.2546042409497926