BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975253.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 = 5,657,586 number of mapped reads = 5,597,008 (98.93%) number of supplementary alignments = 16,757 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,797,597 number of mapped paired reads (second in pair) = 2,799,411 number of mapped paired reads (both in pair) = 5,582,590 number of mapped paired reads (singletons) = 14,418 number of mapped bases = 516,692,177 bp number of sequenced bases = 516,441,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,097 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 53,709.6347 std insert size = 2,225,721.3708 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.7831 >>>>>>> ACTG content number of A's = 154,200,039 bp (29.86%) number of C's = 99,674,612 bp (19.3%) number of T's = 153,824,597 bp (29.79%) number of G's = 108,735,040 bp (21.05%) number of N's = 7,568 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 3,712,061 number of insertions = 83,903 mapped reads with insertion percentage = 1.48% number of deletions = 153,987 mapped reads with deletion percentage = 2.7% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.1669X std coverageData = 1.7741X There is a 10.98% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% 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% 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 43867716 0.17599842208617808 1.8506258257540904 chr2 243199373 41793678 0.1718494479835686 1.6556160423351862 chr3 198022430 31000302 0.15654944745400812 0.5944502646257033 chr4 191154276 24827583 0.12988243590219242 0.7540221840976892 chr5 180915260 39051920 0.21585752357208562 0.6122138904767351 chr6 171115067 42842082 0.2503700156339827 2.6162769983833356 chr7 159138663 31979659 0.20095467937920278 2.324661420357033 chr8 146364022 20170480 0.13781036981888897 0.6064516769045346 chr9 141213431 20079421 0.14219200580148783 1.3903782514626422 chr10 135534747 21008700 0.15500600742627277 4.9613491003613515 chr11 135006516 18254979 0.13521554026325663 1.2392325456094804 chr12 133851895 22618589 0.1689822097774559 0.5339520030924813 chr13 115169878 28587028 0.2482161872221485 0.6874959737866974 chr14 107349540 15588545 0.14521296504856937 0.5203133597710842 chr15 102531392 8118754 0.07918310520937821 0.3588931207170643 chr16 90354753 19036627 0.2106876104237704 3.342510335560075 chr17 81195210 12559976 0.1546886324944538 2.192439916788747 chr18 78077248 9035763 0.11572850262345312 1.827347754600962 chr19 59128983 5007311 0.08468454463355136 1.002883105119035 chr20 63025520 12028721 0.19085476803682064 0.5915810812772382 chr21 48129895 5819971 0.12092216282624343 0.5080238978510605 chr22 51304566 3033660 0.05913040956237696 0.31570299905422256 chrMT 16571 24688 1.4898316335767305 1.6444755999995264 chrX 155270560 39421389 0.25388836750508276 0.9851415775979395 chrY 59373566 934635 0.015741601237156615 0.613873129942873