BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472450.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 = 18,733,818 number of mapped reads = 18,595,335 (99.26%) number of supplementary alignments = 71,217 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,317,846 number of mapped paired reads (second in pair) = 9,277,489 number of mapped paired reads (both in pair) = 18,512,036 number of mapped paired reads (singletons) = 83,299 number of mapped bases = 1,821,278,622 bp number of sequenced bases = 1,821,076,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,055,270 duplication rate = 47.81% >>>>>>> Insert size mean insert size = 16,403.1457 std insert size = 1,276,893.4739 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.6644 >>>>>>> ACTG content number of A's = 493,082,419 bp (27.08%) number of C's = 418,731,921 bp (22.99%) number of T's = 494,376,915 bp (27.15%) number of G's = 414,655,357 bp (22.77%) number of N's = 230,035 bp (0.01%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 9,702,962 number of insertions = 104,566 mapped reads with insertion percentage = 0.56% number of deletions = 86,717 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.5883X std coverageData = 19.5095X There is a 4.95% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 155225353 0.6227681695525245 17.920385117411122 chr2 243199373 156091138 0.6418237681887444 22.078036826343833 chr3 198022430 137572165 0.6947302131379763 17.424807906905787 chr4 191154276 43603413 0.22810587297560636 8.779422446189079 chr5 180915260 77954945 0.43089203752077077 19.509502989574607 chr6 171115067 117998250 0.6895842199565044 15.614815509487524 chr7 159138663 125810095 0.7905690083622231 25.540163306047504 chr8 146364022 141513108 0.9668571966408521 24.52107873702863 chr9 141213431 51764130 0.36656661928991724 13.668308957513043 chr10 135534747 38747961 0.2858894996129664 11.968684884700409 chr11 135006516 66633236 0.493555703637297 17.73179904447989 chr12 133851895 102492942 0.7657190210119924 26.064121203060274 chr13 115169878 61100571 0.5305256205967328 18.378589573633235 chr14 107349540 35925300 0.3346572328116171 11.781126529360426 chr15 102531392 31356968 0.3058279751044441 8.34645921203193 chr16 90354753 122789804 1.35897448582478 36.07342405652257 chr17 81195210 79187370 0.975271447662984 26.488892427613195 chr18 78077248 7379920 0.0945207495018267 3.2934787512460817 chr19 59128983 46326931 0.7834893930105309 18.570901231843983 chr20 63025520 72626049 1.1523276444208632 32.121308178964675 chr21 48129895 17091447 0.3551108308048459 22.591369086642857 chr22 51304566 28875654 0.5628281506172375 20.744217476911327 chrMT 16571 658 0.03970792348077967 0.23713945427579708 chrX 155270560 102691231 0.6613696182972484 18.748145830589788 chrY 59373566 519983 0.008757819936232229 0.9493760287117514