BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818902.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,042,128 number of mapped reads = 2,012,849 (98.57%) number of supplementary alignments = 25,770 (1.26%) number of secondary alignments = 0 number of mapped bases = 186,510,232 bp number of sequenced bases = 186,392,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 454,687 duplication rate = 18.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2666 >>>>>>> ACTG content number of A's = 52,621,907 bp (28.23%) number of C's = 39,452,446 bp (21.17%) number of T's = 53,120,318 bp (28.5%) number of G's = 41,194,565 bp (22.1%) number of N's = 2,799 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,128,496 number of insertions = 23,764 mapped reads with insertion percentage = 1.13% number of deletions = 59,020 mapped reads with deletion percentage = 2.86% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.8008X There is a 4.1% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 17733000 0.07114525905233351 1.217839522106389 chr2 243199373 14253745 0.05860929995078565 1.1414645747627559 chr3 198022430 11562113 0.05838789575504149 0.33085724098118074 chr4 191154276 9258567 0.04843505044061897 0.4258434458165701 chr5 180915260 8176613 0.045195817091383005 0.30626639387928734 chr6 171115067 9241926 0.05401000719591805 0.3611567939468486 chr7 159138663 16808371 0.10562091375620015 1.8393073278161414 chr8 146364022 16044923 0.10962340868167725 0.6026742477506719 chr9 141213431 6846296 0.04848190396280365 0.6525609880943534 chr10 135534747 8745312 0.06452450160253001 1.066204493506883 chr11 135006516 8233560 0.06098638972358934 0.4496318462076828 chr12 133851895 7283206 0.054412423522281844 0.32312276801268297 chr13 115169878 5686507 0.04937495027996817 0.30015532959531915 chr14 107349540 5467153 0.05092851818461448 0.34913610929665295 chr15 102531392 5205078 0.05076570110352154 0.3074238535356485 chr16 90354753 4861030 0.05379938341483818 0.8472582885288533 chr17 81195210 4812678 0.059272930016438165 0.48219657118810577 chr18 78077248 3636197 0.046571787468738655 0.7765208130103874 chr19 59128983 2472308 0.04181211775619412 1.095833309311574 chr20 63025520 7973579 0.12651349802429238 0.5436431814477399 chr21 48129895 1836636 0.03815998351959837 0.3326327710009284 chr22 51304566 1768022 0.03446129921457673 0.29116616037883214 chrMT 16571 365146 22.035242290748897 14.429069061578067 chrX 155270560 7496190 0.048278244117880426 0.3772077514323391 chrY 59373566 742076 0.012498423961936192 0.9883735921510804