BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,859,036 number of mapped reads = 2,624,789 (91.81%) number of supplementary alignments = 26,650 (0.93%) number of secondary alignments = 0 number of mapped bases = 175,949,672 bp number of sequenced bases = 175,885,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,419 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8833 >>>>>>> ACTG content number of A's = 49,329,729 bp (28.05%) number of C's = 33,085,809 bp (18.81%) number of T's = 54,666,631 bp (31.08%) number of G's = 38,778,368 bp (22.05%) number of N's = 24,545 bp (0.01%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,419,433 number of insertions = 13,911 mapped reads with insertion percentage = 0.53% number of deletions = 39,924 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.4558X There is a 4.77% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 15547248 0.062375964952961944 0.8230056999710731 chr2 243199373 13607287 0.05595115987408405 0.5474598507802436 chr3 198022430 10916138 0.05512576529840584 0.2769980670759565 chr4 191154276 12633910 0.06609274071378869 0.3056172733233186 chr5 180915260 10076403 0.05569681076101596 0.2719782244399924 chr6 171115067 9432997 0.05512663008220077 0.3428635189400729 chr7 159138663 9937726 0.062446961741786156 0.4282332198167199 chr8 146364022 9386370 0.06413030929144595 0.7096508694941402 chr9 141213431 8045106 0.05697125225999218 0.42309735996983017 chr10 135534747 7459820 0.055039907958067756 0.5118666668962034 chr11 135006516 8097552 0.0599789716816335 0.3979837220276608 chr12 133851895 7232634 0.05403460294678682 0.27189697263274426 chr13 115169878 5844939 0.05075058775350964 0.2582326142311371 chr14 107349540 5103470 0.04754067879564272 0.27231363022056715 chr15 102531392 4906389 0.04785255426942804 0.25340002833699254 chr16 90354753 5298788 0.05864426412631552 0.3185799589330155 chr17 81195210 4469419 0.05504535304484095 0.3092999945467887 chr18 78077248 4790136 0.061351240248631714 0.7776421625634875 chr19 59128983 3564063 0.06027607476353855 0.6074336709797462 chr20 63025520 3892289 0.061757348451865215 0.29222448748684854 chr21 48129895 2191817 0.04553961732100184 0.2646424085222582 chr22 51304566 1533534 0.0298907898373022 0.19660425905707188 chrMT 16571 4237 0.2556876470943214 0.5243253861585909 chrX 155270560 11554768 0.07441699186246253 0.35390792127511095 chrY 59373566 422632 0.007118184546974995 0.13989530723434748