BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083654.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,551,627 number of mapped reads = 1,211,101 (78.05%) number of supplementary alignments = 8,051 (0.52%) number of secondary alignments = 0 number of mapped bases = 78,300,483 bp number of sequenced bases = 78,274,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,187 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3802 >>>>>>> ACTG content number of A's = 23,527,181 bp (30.06%) number of C's = 14,516,421 bp (18.55%) number of T's = 22,829,185 bp (29.17%) number of G's = 17,390,739 bp (22.22%) number of N's = 10,689 bp (0.01%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 693,269 number of insertions = 5,725 mapped reads with insertion percentage = 0.47% number of deletions = 16,393 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.267X There is a 2.35% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9156098 0.03673450426428426 0.6392608902583763 chr2 243199373 6338545 0.026063163411198433 0.22523671823812427 chr3 198022430 6660955 0.03363737633156002 0.19388705150135882 chr4 191154276 3557493 0.0186105855147075 0.1442903747327729 chr5 180915260 3934669 0.02174868499207861 0.15454091593071806 chr6 171115067 4772837 0.02789255840340465 0.20111023706535264 chr7 159138663 5779523 0.03631752894643837 0.3618551604264186 chr8 146364022 5379667 0.036755391977408215 0.2964810765984359 chr9 141213431 3113692 0.022049545697958434 0.18827850057782286 chr10 135534747 3556847 0.02624306370675558 0.21740614518177073 chr11 135006516 2545406 0.018853949241975847 0.15720362389293846 chr12 133851895 2697032 0.02014937479966197 0.14952366514715026 chr13 115169878 2441110 0.021195733141264595 0.15158441069142503 chr14 107349540 1745016 0.016255458570199742 0.1345912737913715 chr15 102531392 1886930 0.018403436871314495 0.14228111622515585 chr16 90354753 2021256 0.02237022329085444 0.16113772577079938 chr17 81195210 1499687 0.018470141280501645 0.14717338004059127 chr18 78077248 2211731 0.028327471275626927 0.28006902451543 chr19 59128983 2155303 0.0364508721552001 0.358334970303813 chr20 63025520 1593447 0.025282568077185243 0.1679210156923676 chr21 48129895 1127187 0.0234196854158938 0.1617834501222894 chr22 51304566 454851 0.008865702128734507 0.09795670833696395 chrMT 16571 4199 0.25339448434011225 0.4807569852558784 chrX 155270560 3518707 0.022661778253392016 0.16137772921247462 chrY 59373566 148295 0.002497660322440461 0.0595196511087098