BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083675.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 = 1,878,565 number of mapped reads = 1,339,641 (71.31%) number of supplementary alignments = 8,204 (0.44%) number of secondary alignments = 0 number of mapped bases = 83,498,664 bp number of sequenced bases = 83,471,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,396 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5116 >>>>>>> ACTG content number of A's = 23,993,181 bp (28.74%) number of C's = 15,434,435 bp (18.49%) number of T's = 24,959,452 bp (29.9%) number of G's = 19,073,485 bp (22.85%) number of N's = 11,404 bp (0.01%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 734,590 number of insertions = 5,968 mapped reads with insertion percentage = 0.44% number of deletions = 16,777 mapped reads with deletion percentage = 1.24% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.253X There is a 2.48% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 7687484 0.030842386547153277 0.5225890109103591 chr2 243199373 9143477 0.037596630645918644 0.2594443336911672 chr3 198022430 7213296 0.03642666136356371 0.2036322307499537 chr4 191154276 4167465 0.02180157874156056 0.1579672824804467 chr5 180915260 4157786 0.0229819529872715 0.16138065090579734 chr6 171115067 5846527 0.034167225028757985 0.23413313875695482 chr7 159138663 4768349 0.029963485366218012 0.31534130462163007 chr8 146364022 5445020 0.03720190198107565 0.29420095487266873 chr9 141213431 3684754 0.02609350947644633 0.19997259668336945 chr10 135534747 4261125 0.03143935480987765 0.23354386266515637 chr11 135006516 2769351 0.02051272103044271 0.18730667374489215 chr12 133851895 3092831 0.023106366928910493 0.16122455846810038 chr13 115169878 2355896 0.02045583481472473 0.15094563574448208 chr14 107349540 1910061 0.01779291275957028 0.14317901294668456 chr15 102531392 2162912 0.021095119824375348 0.1540870623649519 chr16 90354753 2307785 0.025541379101550972 0.1745030448147328 chr17 81195210 1770031 0.021799697297414464 0.16346874718647036 chr18 78077248 2269078 0.02906196181504758 0.3341653358851079 chr19 59128983 1968120 0.03328519957801405 0.3619049448533115 chr20 63025520 1454133 0.02307213014664536 0.16295671084512886 chr21 48129895 1319507 0.027415538720788814 0.17733561821511856 chr22 51304566 678656 0.013227984425401825 0.12078825518570556 chrMT 16571 37034 2.234868143141633 1.9863282436705618 chrX 155270560 2867750 0.01846937371772215 0.1543616130343886 chrY 59373566 160236 0.002698776758667317 0.06367798218304346