BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818842.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 = 802,718 number of mapped reads = 779,774 (97.14%) number of supplementary alignments = 11,985 (1.49%) number of secondary alignments = 0 number of mapped bases = 72,232,123 bp number of sequenced bases = 72,191,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,752 duplication rate = 7.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2232 >>>>>>> ACTG content number of A's = 20,689,815 bp (28.66%) number of C's = 15,767,104 bp (21.84%) number of T's = 20,542,576 bp (28.46%) number of G's = 15,190,921 bp (21.04%) number of N's = 974 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 424,353 number of insertions = 9,184 mapped reads with insertion percentage = 1.14% number of deletions = 20,496 mapped reads with deletion percentage = 2.57% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.3198X There is a 1.98% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% 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 6822585 0.027372389174508818 0.47424187199453605 chr2 243199373 5479949 0.022532743125123107 0.3686223236798131 chr3 198022430 4300508 0.021717277179155916 0.16579722653038098 chr4 191154276 3709756 0.019407130604810537 0.2135494596372279 chr5 180915260 3216701 0.017780152984330895 0.15189154222763226 chr6 171115067 3534635 0.020656480238528615 0.17008450426319485 chr7 159138663 6471394 0.04066512736757126 0.6940742515795872 chr8 146364022 6262383 0.042786354969119395 0.2904033007290264 chr9 141213431 2668845 0.01889937083959103 0.2867058712118021 chr10 135534747 3519948 0.025970816177492848 0.5330733542561308 chr11 135006516 3168844 0.02347178561366623 0.2074754051330795 chr12 133851895 2775105 0.0207326538036686 0.16107231671628475 chr13 115169878 2211285 0.01920020267799537 0.15511062986029958 chr14 107349540 2080139 0.019377251174061853 0.16177369530467656 chr15 102531392 1987371 0.019383049047066482 0.1544394851507586 chr16 90354753 1891899 0.020938566452613733 0.2503201432403288 chr17 81195210 1815706 0.02236223048133012 0.2184737927112862 chr18 78077248 1423470 0.018231559595952972 0.32766092135721914 chr19 59128983 1253236 0.021194952735784412 0.41942964235801233 chr20 63025520 2965671 0.04705508181447769 0.25436152342350293 chr21 48129895 710762 0.014767578445787176 0.16355758398396514 chr22 51304566 658508 0.012835270841195694 0.13135236497940306 chrMT 16571 93620 5.6496288697121475 4.172781033371531 chrX 155270560 2906535 0.018719163504015184 0.18122386890169395 chrY 59373566 303268 0.005107794940260115 0.34625266731406995