BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818836.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 = 2,175,816 number of mapped reads = 2,129,441 (97.87%) number of supplementary alignments = 36,454 (1.68%) number of secondary alignments = 0 number of mapped bases = 197,088,713 bp number of sequenced bases = 196,965,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 582,527 duplication rate = 23.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4282 >>>>>>> ACTG content number of A's = 55,225,119 bp (28.04%) number of C's = 42,319,870 bp (21.49%) number of T's = 58,461,483 bp (29.68%) number of G's = 40,955,827 bp (20.79%) number of N's = 2,752 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,202,571 number of insertions = 29,267 mapped reads with insertion percentage = 1.34% number of deletions = 64,670 mapped reads with deletion percentage = 2.97% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.0637X std coverageData = 0.7111X There is a 4.09% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 18561532 0.07446935107134597 1.0393066408031724 chr2 243199373 14989399 0.06163420084146352 1.0525844200551393 chr3 198022430 12467763 0.06296136755821045 0.35857061092247217 chr4 191154276 10112666 0.052903163934454704 0.42063290831831585 chr5 180915260 8842827 0.04887828146724605 0.3342402081326872 chr6 171115067 9832800 0.05746308710500636 0.3890234141032999 chr7 159138663 17670743 0.11103991114968711 1.5039029078821926 chr8 146364022 17436023 0.11912779357757741 0.6451804025680136 chr9 141213431 7244945 0.0513049286367102 0.6054598907252733 chr10 135534747 9036417 0.06667232720772334 0.9218243134959208 chr11 135006516 8648647 0.06406095984285677 0.440991465330911 chr12 133851895 7698247 0.05751317155427647 0.3468923308137547 chr13 115169878 6210391 0.053923743845591295 0.3274427672243614 chr14 107349540 5715818 0.05324492308024795 0.36079327721188853 chr15 102531392 5385115 0.05252162186581842 0.32379657086460634 chr16 90354753 4759994 0.052681168858930975 0.7581967838553993 chr17 81195210 4738672 0.05836147230852658 0.4589143284000992 chr18 78077248 3779587 0.048408301993430915 0.6701746777199374 chr19 59128983 3266319 0.05524057466031506 0.8693802984665039 chr20 63025520 8015196 0.12717381784394638 0.55004254033528 chr21 48129895 1878412 0.039027967960453686 0.34027456931709565 chr22 51304566 1767691 0.03445484754709747 0.2949003491816338 chrMT 16571 229730 13.86337577695975 9.298983922731832 chrX 155270560 8101881 0.052179118823297864 0.3994884160572189 chrY 59373566 697898 0.011754355465191362 0.8720448185118062