BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046486.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 41,899,884 number of mapped reads = 41,743,436 (99.63%) number of supplementary alignments = 179,518 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,910,330 number of mapped paired reads (second in pair) = 20,833,106 number of mapped paired reads (both in pair) = 41,632,246 number of mapped paired reads (singletons) = 111,190 number of mapped bases = 4,106,084,227 bp number of sequenced bases = 4,105,291,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,703,513 duplication rate = 22.18% >>>>>>> Insert size mean insert size = 15,162.9988 std insert size = 1,222,407.5251 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.4334 >>>>>>> ACTG content number of A's = 1,130,608,620 bp (27.54%) number of C's = 920,535,859 bp (22.42%) number of T's = 1,136,417,216 bp (27.68%) number of G's = 917,338,090 bp (22.35%) number of N's = 391,714 bp (0.01%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 16,197,173 number of insertions = 247,649 mapped reads with insertion percentage = 0.58% number of deletions = 282,936 mapped reads with deletion percentage = 0.66% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 1.3264X std coverageData = 219.1273X There is a 4.27% of reference with a coverageData >= 1X There is a 2.91% of reference with a coverageData >= 2X There is a 1.9% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 1.08% of reference with a coverageData >= 5X There is a 0.85% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 750485579 3.010967739976062 424.23332866993115 chr2 243199373 94430338 0.38828364084639316 39.88266504324622 chr3 198022430 73525844 0.37130058448429304 41.92689361458342 chr4 191154276 310734848 1.625571002136515 234.49486868672034 chr5 180915260 618997142 3.421475568174846 422.9599112020282 chr6 171115067 109555847 0.6402466417524765 108.92117618621688 chr7 159138663 504631414 3.1710170519655554 359.3917828821227 chr8 146364022 344430750 2.353247371133324 293.37372349135615 chr9 141213431 243063887 1.7212519041478427 231.15965004955308 chr10 135534747 43396650 0.3201883720637336 17.638310175516423 chr11 135006516 104089455 0.7709957866033667 66.08254765625287 chr12 133851895 261376219 1.9527270719626346 221.67454606950108 chr13 115169878 228682552 1.9856107861814354 241.83197989129962 chr14 107349540 14367838 0.1338416354648562 3.521916918523034 chr15 102531392 23871867 0.2328249576480928 7.057631328965022 chr16 90354753 118932700 1.3162860397615164 126.80449482672613 chr17 81195210 122418305 1.5077035332502988 145.592992873392 chr18 78077248 6148657 0.078750944193115 1.756071466006678 chr19 59128983 61622883 1.0421772855453983 45.802372868972554 chr20 63025520 31955100 0.5070184268213892 39.25292562852547 chr21 48129895 2381082 0.049471996562635345 1.2382453956362047 chr22 51304566 18438980 0.3594023190840363 40.854449012999474 chrMT 16571 764567 46.13885703940619 15.739538760281288 chrX 155270560 17366233 0.11184498207515964 8.744906227650402 chrY 59373566 415490 0.006997895326010905 0.25499123350138825