BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505982.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,706,033 number of mapped reads = 6,561,915 (75.37%) number of supplementary alignments = 224 (0%) number of secondary alignments = 0 number of mapped bases = 306,351,143 bp number of sequenced bases = 306,295,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 515,852 duplication rate = 5.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4146 >>>>>>> ACTG content number of A's = 92,208,710 bp (30.1%) number of C's = 61,618,432 bp (20.12%) number of T's = 90,090,806 bp (29.41%) number of G's = 62,375,952 bp (20.36%) number of N's = 1,328 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,415,629 number of insertions = 13,542 mapped reads with insertion percentage = 0.21% number of deletions = 41,180 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.099X std coverageData = 0.8842X There is a 6.04% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.13% 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 0.01% 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% 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 23941780 0.09605504653888104 1.6879832786135909 chr2 243199373 25629546 0.10538491807707087 0.7482257310348751 chr3 198022430 20564258 0.10384812467961331 0.490764274442176 chr4 191154276 20333056 0.10636987267812936 0.493400350497704 chr5 180915260 18965348 0.1048300071536254 0.49141706471763175 chr6 171115067 18810836 0.10993091566857757 0.7358598154560554 chr7 159138663 17256836 0.10843899071842775 1.1580070283270736 chr8 146364022 16580564 0.11328305804550794 1.340834549642585 chr9 141213431 13066096 0.09252728941909215 0.6727868014736065 chr10 135534747 14100052 0.10403274667270379 0.854204610279305 chr11 135006516 14493876 0.10735686268653877 0.773661142161506 chr12 133851895 13822629 0.10326808596919752 0.5156074966907627 chr13 115169878 9790599 0.08501006660786772 0.42956547102093284 chr14 107349540 9309500 0.08672137766030483 1.0198059861151232 chr15 102531392 8637364 0.08424116586654748 0.42703712623634266 chr16 90354753 8254485 0.0913564004762428 0.512828851216765 chr17 81195210 7254327 0.08934427289491585 0.5062790647177492 chr18 78077248 8137226 0.10422019485113 1.5160571376429952 chr19 59128983 5353028 0.09053137274490244 1.1798900134403905 chr20 63025520 6099181 0.0967731960006042 0.4875716013148362 chr21 48129895 3711894 0.07712242048315293 0.468560098706228 chr22 51304566 3441813 0.06708590030758665 0.37689214326093523 chrMT 16571 667374 40.27361052441012 23.530035468244154 chrX 155270560 17255601 0.11113247095907942 0.6055384258459823 chrY 59373566 873874 0.014718233363311881 0.22986776921907282