BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975278.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,636,052 number of mapped reads = 2,604,408 (98.8%) number of supplementary alignments = 29,790 (1.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,304,441 number of mapped paired reads (second in pair) = 1,299,967 number of mapped paired reads (both in pair) = 2,595,106 number of mapped paired reads (singletons) = 9,302 number of mapped bases = 348,498,659 bp number of sequenced bases = 348,259,088 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 437,420 duplication rate = 16.12% >>>>>>> Insert size mean insert size = 62,128.1195 std insert size = 2,297,296.6358 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.5191 >>>>>>> ACTG content number of A's = 104,308,455 bp (29.95%) number of C's = 68,332,730 bp (19.62%) number of T's = 103,503,063 bp (29.72%) number of G's = 72,091,830 bp (20.7%) number of N's = 23,010 bp (0.01%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 3,271,454 number of insertions = 68,849 mapped reads with insertion percentage = 2.5% number of deletions = 111,088 mapped reads with deletion percentage = 4.1% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.1126X std coverageData = 1.4281X There is a 6.08% of reference with a coverageData >= 1X There is a 3.53% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 25708754 0.10314419236692694 1.367573762455122 chr2 243199373 25374939 0.10433801159512035 1.658944136738772 chr3 198022430 30204951 0.1525329782085797 0.5795409192115019 chr4 191154276 28640392 0.1498286755562821 1.3293432978077 chr5 180915260 17657701 0.0976020541329681 0.44499385522726426 chr6 171115067 31110804 0.18181218372780697 1.1177612241928458 chr7 159138663 16312190 0.10250299765305933 1.042512142880243 chr8 146364022 14454415 0.09875661246860243 0.5944327874188846 chr9 141213431 16226696 0.11490901315187221 2.582974467743759 chr10 135534747 15781433 0.1164382813213205 3.3620801834320897 chr11 135006516 10265895 0.07603999646950374 0.9811661953596044 chr12 133851895 18186142 0.13586764684952723 0.528088216431684 chr13 115169878 12885923 0.11188622601475709 0.4839574394154871 chr14 107349540 12298930 0.11456900513965873 0.5090973104295085 chr15 102531392 10860587 0.10592450554070308 0.46333668328276745 chr16 90354753 13793751 0.1526621515970499 2.772631555985384 chr17 81195210 5575216 0.06866434608642555 0.7732066489894108 chr18 78077248 8253041 0.10570353350568913 2.2405554111335575 chr19 59128983 4895002 0.08278515461698369 0.9637933834318461 chr20 63025520 7906824 0.12545432389927128 0.6715910013051642 chr21 48129895 5288268 0.10987491246344917 0.823513858387041 chr22 51304566 2462033 0.047988574740111825 0.3195906157230489 chrMT 16571 79399 4.791442882143504 3.907887165892203 chrX 155270560 9213184 0.05933632235241504 0.457560964567646 chrY 59373566 5062189 0.08525997916311781 2.206265613787052