BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006096.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,056,634 number of mapped reads = 7,851,931 (86.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,993,678 number of mapped paired reads (second in pair) = 3,858,253 number of mapped paired reads (both in pair) = 7,078,570 number of mapped paired reads (singletons) = 773,361 number of mapped bases = 303,028,261 bp number of sequenced bases = 302,995,354 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 531,080 duplication rate = 6.09% >>>>>>> Insert size mean insert size = 68,518.4127 std insert size = 2,545,223.8243 median insert size = 117 >>>>>>> Mapping quality mean mapping quality = 47.2995 >>>>>>> ACTG content number of A's = 82,323,098 bp (27.17%) number of C's = 65,576,719 bp (21.64%) number of T's = 85,076,382 bp (28.08%) number of G's = 70,006,887 bp (23.1%) number of N's = 12,268 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,714,205 number of insertions = 10,032 mapped reads with insertion percentage = 0.13% number of deletions = 26,135 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 0.5501X There is a 5.7% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% 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 25817932 0.10358221735383359 0.6109098813119032 chr2 243199373 26678832 0.10969942755567877 0.5992817846893599 chr3 198022430 20674223 0.10440344055973862 0.49761292374805755 chr4 191154276 18296662 0.0957167288269293 0.49574568050473444 chr5 180915260 18582829 0.10271565262101162 0.49470329328718066 chr6 171115067 17215449 0.10060744095667508 0.5565830453764646 chr7 159138663 16263750 0.10219860902061242 0.6712953142710916 chr8 146364022 15306774 0.10458016793225319 0.5980790505068021 chr9 141213431 13187932 0.0933900685410016 0.5032063504055049 chr10 135534747 14278887 0.1053522238101791 0.5170572419868109 chr11 135006516 14045717 0.10403732661318361 0.7626164499355048 chr12 133851895 13992500 0.10453718268239684 0.5018068503660659 chr13 115169878 9507545 0.08255235800458172 0.4453063800271892 chr14 107349540 9802984 0.09131836056307274 0.4759974365071322 chr15 102531392 9266942 0.09038150969412373 0.4683885401576431 chr16 90354753 9659794 0.10690963872149592 0.5475479014997724 chr17 81195210 9115775 0.11226986173199133 0.5736865691698254 chr18 78077248 7836557 0.10036927787208894 0.6576656192656347 chr19 59128983 6726937 0.11376716897024933 0.6458346689576379 chr20 63025520 7238024 0.11484274941325355 0.5316680056320312 chr21 48129895 4219223 0.08766324962894684 0.5124685542099433 chr22 51304566 4167230 0.08122532407739304 0.4688556961706532 chrMT 16571 17626 1.0636654396234386 2.136264306269442 chrX 155270560 9090712 0.05854755724459292 0.39593849138300363 chrY 59373566 2037425 0.03431535508579694 0.31893104400924555