BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472498.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 = 17,827,816 number of mapped reads = 17,592,135 (98.68%) number of supplementary alignments = 63,184 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,821,961 number of mapped paired reads (second in pair) = 8,770,174 number of mapped paired reads (both in pair) = 17,481,254 number of mapped paired reads (singletons) = 110,881 number of mapped bases = 1,733,038,230 bp number of sequenced bases = 1,732,806,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,310,260 duplication rate = 46.08% >>>>>>> Insert size mean insert size = 22,990.9557 std insert size = 1,495,317.6359 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 54.9596 >>>>>>> ACTG content number of A's = 477,688,826 bp (27.57%) number of C's = 391,663,776 bp (22.6%) number of T's = 474,451,672 bp (27.38%) number of G's = 388,733,673 bp (22.43%) number of N's = 269,051 bp (0.02%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,641,293 number of insertions = 92,336 mapped reads with insertion percentage = 0.52% number of deletions = 89,511 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.5598X std coverageData = 21.4152X There is a 5.31% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 200218217 0.8032807147950897 34.34729845846935 chr2 243199373 115992519 0.47694415314138167 18.86488832006489 chr3 198022430 200614827 1.013091431107072 23.148130108495717 chr4 191154276 64160832 0.33564947299426356 12.71824973684548 chr5 180915260 98001182 0.541696604255495 20.846041900871565 chr6 171115067 89200684 0.5212906470708392 15.180901106047559 chr7 159138663 72874923 0.45793348785392274 15.76371322908326 chr8 146364022 81994409 0.5602087717977577 17.126186369217656 chr9 141213431 103709368 0.7344157511476369 22.391565087612378 chr10 135534747 52624339 0.38827193885565003 15.933117538183767 chr11 135006516 87622479 0.6490240737713726 37.15761801411337 chr12 133851895 96113463 0.7180582912180661 25.151398457603253 chr13 115169878 40812490 0.3543677453578617 17.85862684465859 chr14 107349540 24890579 0.23186479420405529 7.791283643381863 chr15 102531392 38649132 0.37694925667253204 14.53695392052622 chr16 90354753 59291570 0.6562086446077717 24.46707030161307 chr17 81195210 67751503 0.8344273387555744 23.905467131666242 chr18 78077248 24558660 0.314543104797956 9.935576885965931 chr19 59128983 46324277 0.7834445080849776 21.32947707152883 chr20 63025520 39623537 0.6286903622532587 17.851138068013494 chr21 48129895 8884570 0.184595665542175 8.215790797419402 chr22 51304566 17189520 0.3350485412935761 13.39883321210581 chrMT 16571 1575 0.09504556152314284 0.38929176772397894 chrX 155270560 99191560 0.6388304389447684 24.381357791595903 chrY 59373566 2742015 0.046182420641536 2.185110106729128