BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006395.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 = 8,100,946 number of mapped reads = 6,864,399 (84.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,478,445 number of mapped paired reads (second in pair) = 3,385,954 number of mapped paired reads (both in pair) = 6,293,084 number of mapped paired reads (singletons) = 571,315 number of mapped bases = 265,851,089 bp number of sequenced bases = 265,817,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 328,493 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 66,368.0227 std insert size = 2,486,157.7413 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 48.3586 >>>>>>> ACTG content number of A's = 74,878,894 bp (28.17%) number of C's = 56,746,663 bp (21.35%) number of T's = 75,544,270 bp (28.42%) number of G's = 58,636,926 bp (22.06%) number of N's = 11,146 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 983,213 number of insertions = 7,101 mapped reads with insertion percentage = 0.1% number of deletions = 24,502 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.07% >>>>>>> Coverage mean coverageData = 0.0859X std coverageData = 0.4952X There is a 7.08% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 22483441 0.09020415239005564 0.6457630307124383 chr2 243199373 22203959 0.09129940890102542 0.43319301441904895 chr3 198022430 18449231 0.09316738007911528 0.35351111359304965 chr4 191154276 16764908 0.08770354684610875 0.388366285876543 chr5 180915260 16355306 0.09040313127814646 0.34930494415724495 chr6 171115067 15155033 0.08856632712536062 0.3832501660623796 chr7 159138663 13812371 0.08679456481295184 0.505324176898741 chr8 146364022 13742366 0.09389169423070377 1.2312470805566702 chr9 141213431 11483469 0.08131994895018166 0.3801143821528983 chr10 135534747 12476455 0.09205355287969069 0.5045380549954864 chr11 135006516 12049510 0.08925132176583239 0.4070886147843189 chr12 133851895 11565278 0.08640354325951081 0.34416889086052044 chr13 115169878 8380359 0.07276519820573223 0.31414049351807455 chr14 107349540 7991834 0.07444683973494437 0.35891883240552597 chr15 102531392 7811554 0.07618694965147844 0.32018144842622454 chr16 90354753 8104111 0.08969213827633395 0.43032917581175295 chr17 81195210 7260899 0.08942521363021291 0.3635181254767029 chr18 78077248 6833405 0.08752107912410027 0.5954894458159883 chr19 59128983 5006006 0.08466247423873331 0.49473665391940996 chr20 63025520 5717336 0.09071461845931617 0.3639082483287981 chr21 48129895 3578326 0.07434726379519424 0.3630772652434382 chr22 51304566 3246139 0.06327193178088672 0.29966759656890135 chrMT 16571 1548 0.09341620903988897 0.37379877879619217 chrX 155270560 14710049 0.09473817187237554 0.38887357663073563 chrY 59373566 668196 0.011254099172685703 0.2755313150294208