BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549050.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,781,649 number of mapped reads = 3,282,295 (86.8%) number of secondary alignments = 0 number of mapped bases = 129,916,427 bp number of sequenced bases = 129,902,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,905 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6412 >>>>>>> ACTG content number of A's = 36,902,699 bp (28.41%) number of C's = 27,558,266 bp (21.21%) number of T's = 37,605,090 bp (28.95%) number of G's = 27,835,347 bp (21.43%) number of N's = 1,125 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 328,686 number of insertions = 3,682 mapped reads with insertion percentage = 0.11% number of deletions = 10,287 mapped reads with deletion percentage = 0.31% homopolymer indels = 41.53% >>>>>>> Coverage mean coverageData = 0.042X std coverageData = 0.3815X There is a 3.69% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10584425 0.042464989485422384 0.5613523171126634 chr2 243199373 11044927 0.04541511297399603 0.29365117319568307 chr3 198022430 8872083 0.0448034245413512 0.23411566757093072 chr4 191154276 8581021 0.04489055217367986 0.24364289424198424 chr5 180915260 8105309 0.04480168781782145 0.23558118403908918 chr6 171115067 7614430 0.04449888682216394 0.24254155576112332 chr7 159138663 7341717 0.04613408747816362 0.4378893702183257 chr8 146364022 6837995 0.04671909740222908 1.0502471760887828 chr9 141213431 5559961 0.039372749182760104 0.2796392971597578 chr10 135534747 6154422 0.045408444227220936 0.2874392953617088 chr11 135006516 5994396 0.04440079025519035 0.2761408252969897 chr12 133851895 5947714 0.04443503769595492 0.23584268549119514 chr13 115169878 4206886 0.03652765873382274 0.21048846158876214 chr14 107349540 4043440 0.037666113892989204 0.23447161592430207 chr15 102531392 3742340 0.03649945569840698 0.2109346531303164 chr16 90354753 3735686 0.041344653999552186 0.23612791988102214 chr17 81195210 3514757 0.043287738279142327 0.23776578562623518 chr18 78077248 3494911 0.04476222061515283 0.4491191309920703 chr19 59128983 2754404 0.046582976067760205 0.5163147269217822 chr20 63025520 2766115 0.04388880885076395 0.2383635510746733 chr21 48129895 1719741 0.03573124354416314 0.23690672666188076 chr22 51304566 1557953 0.030366751372577636 0.23944341495303215 chrMT 16571 10878 0.6564480115865066 1.0926015373811944 chrX 155270560 4483820 0.02887746395710816 0.21426113545603345 chrY 59373566 1247096 0.02100422939056751 0.24766709835349263