BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240211.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,165,328 number of mapped reads = 1,731,822 (79.98%) number of supplementary alignments = 18,810 (0.87%) number of secondary alignments = 0 number of mapped bases = 113,947,961 bp number of sequenced bases = 113,897,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,114 duplication rate = 8.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4121 >>>>>>> ACTG content number of A's = 32,510,184 bp (28.54%) number of C's = 21,384,272 bp (18.77%) number of T's = 35,823,931 bp (31.45%) number of G's = 24,169,037 bp (21.22%) number of N's = 10,203 bp (0.01%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 895,188 number of insertions = 8,078 mapped reads with insertion percentage = 0.46% number of deletions = 29,140 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3801X There is a 1.92% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 8189088 0.03285483489326994 0.46710284559221504 chr2 243199373 8082117 0.033232474657736884 0.37377201578112046 chr3 198022430 9748761 0.04923058968622898 0.37497996473261885 chr4 191154276 7018155 0.036714611605130926 0.3344649055797898 chr5 180915260 7614106 0.04208658794178004 0.3545895884493433 chr6 171115067 10394676 0.06074670210075656 0.4430906873109258 chr7 159138663 8368229 0.05258451241355471 0.4466643650275402 chr8 146364022 4264212 0.02913429093934027 0.6064948837399304 chr9 141213431 3810267 0.026982327198041098 0.3070839334123986 chr10 135534747 5882379 0.04340126152299528 0.38450685455873007 chr11 135006516 6020491 0.04459407722216904 0.3911425387449166 chr12 133851895 5437043 0.04061984329769855 0.3559170348789422 chr13 115169878 4216028 0.036607037128232434 0.33176495454404104 chr14 107349540 2317381 0.021587246671015078 0.2565064582559521 chr15 102531392 2156209 0.02102974472442547 0.25121751453659535 chr16 90354753 1830117 0.02025479500785089 0.2446967786452322 chr17 81195210 2633282 0.03243149441943681 0.3120013776392159 chr18 78077248 3068918 0.039306175340606264 0.4762650094103111 chr19 59128983 3055926 0.05168237038678646 0.41458295092216546 chr20 63025520 3030792 0.04808832993365227 0.3739720083788161 chr21 48129895 924421 0.019206794446570058 0.23335039841267013 chr22 51304566 1061550 0.020691140823606225 0.23138141692735514 chrMT 16571 9398 0.5671353569488866 1.1769976755365619 chrX 155270560 4588436 0.029551229801708708 0.30187570495695354 chrY 59373566 225979 0.0038060540274774805 0.10628243818002167