BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618636.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 17,930,890 number of mapped reads = 16,986,359 (94.73%) number of supplementary alignments = 48,377 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,652,200 number of mapped paired reads (second in pair) = 8,334,159 number of mapped paired reads (both in pair) = 16,461,232 number of mapped paired reads (singletons) = 525,127 number of mapped bases = 1,614,363,316 bp number of sequenced bases = 1,613,238,626 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,420,487 duplication rate = 25.92% >>>>>>> Insert size mean insert size = 83,526.7568 std insert size = 2,916,064.0756 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.6055 >>>>>>> ACTG content number of A's = 442,915,242 bp (27.46%) number of C's = 351,588,619 bp (21.79%) number of T's = 448,267,666 bp (27.79%) number of G's = 370,406,773 bp (22.96%) number of N's = 60,326 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 18,877,338 number of insertions = 294,339 mapped reads with insertion percentage = 1.7% number of deletions = 820,639 mapped reads with deletion percentage = 4.71% homopolymer indels = 53.31% >>>>>>> Coverage mean coverageData = 0.5215X std coverageData = 2.2933X There is a 15.83% of reference with a coverageData >= 1X There is a 9.44% of reference with a coverageData >= 2X There is a 6.25% of reference with a coverageData >= 3X There is a 4.46% of reference with a coverageData >= 4X There is a 3.26% of reference with a coverageData >= 5X There is a 2.46% of reference with a coverageData >= 6X There is a 1.88% of reference with a coverageData >= 7X There is a 1.47% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.74% of reference with a coverageData >= 11X There is a 0.6% of reference with a coverageData >= 12X There is a 0.49% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 140149806 0.5622846813288381 2.567534006739788 chr2 243199373 136040993 0.5593805252121271 2.7197917873058914 chr3 198022430 104850764 0.5294893310823425 2.1254774522635986 chr4 191154276 81843835 0.42815592050894014 1.8368050788861336 chr5 180915260 92664494 0.5121983297594686 2.0352780705956466 chr6 171115067 88380651 0.5164983572136287 2.002444351612261 chr7 159138663 81458164 0.5118690987117317 2.068472926510661 chr8 146364022 78064159 0.5333562027968868 2.213839082447331 chr9 141213431 69443680 0.49176398808694055 2.4148208888154308 chr10 135534747 79682151 0.5879093941865697 2.162513513101674 chr11 135006516 80645299 0.5973437533933548 2.530310678513835 chr12 133851895 73226553 0.5470714702993185 2.21451760890741 chr13 115169878 44471974 0.3861424078264631 1.6563178093220094 chr14 107349540 50848104 0.4736685783655896 2.017031240928083 chr15 102531392 52312392 0.5102085417898159 2.1050530280997406 chr16 90354753 54860169 0.6071641743074656 3.93439137878226 chr17 81195210 50846102 0.6262204630051452 2.3087046099991655 chr18 78077248 41955344 0.537356849462727 2.4009627046720716 chr19 59128983 34200340 0.5784023039936269 2.3439082937753297 chr20 63025520 43233517 0.6859684299312405 2.486865236007241 chr21 48129895 21231775 0.4411348705414795 2.3043231890685205 chr22 51304566 27642079 0.5387839943914544 2.312304537203887 chrMT 16571 28807 1.7383984068553497 6.623778781763428 chrX 155270560 84066611 0.5414201571759644 2.0193746776540578 chrY 59373566 2215553 0.03731547806981982 1.2703990791016622