BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818792.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 = 1,258,031 number of mapped reads = 1,148,114 (91.26%) number of supplementary alignments = 8,109 (0.64%) number of secondary alignments = 0 number of mapped bases = 78,038,860 bp number of sequenced bases = 78,006,196 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 392,188 duplication rate = 30.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6249 >>>>>>> ACTG content number of A's = 22,535,503 bp (28.89%) number of C's = 15,863,617 bp (20.34%) number of T's = 22,116,407 bp (28.35%) number of G's = 17,486,052 bp (22.42%) number of N's = 4,617 bp (0.01%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 388,847 number of insertions = 7,731 mapped reads with insertion percentage = 0.66% number of deletions = 19,715 mapped reads with deletion percentage = 1.7% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.3471X There is a 1.45% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6537738 0.026229575572451633 0.5216789623847347 chr2 243199373 6930660 0.02849785307629062 0.5503730105113032 chr3 198022430 5333704 0.026934847734168297 0.26105394892177264 chr4 191154276 5206873 0.02723911339550678 0.298802812625944 chr5 180915260 4975603 0.027502395320328422 0.26500985655592857 chr6 171115067 4251763 0.024847391141774793 0.2705491718316049 chr7 159138663 4303412 0.02704190118777107 0.306063276303216 chr8 146364022 4023868 0.027492193402556264 0.29870129781510696 chr9 141213431 3417482 0.024200828319226944 0.288003716199546 chr10 135534747 3814007 0.028140436931645287 0.3875153977799054 chr11 135006516 3677356 0.02723835936926185 0.2833528693390263 chr12 133851895 3431890 0.025639457700617537 0.2656362705521682 chr13 115169878 2555183 0.022186209140553227 0.2352957266798416 chr14 107349540 2449876 0.022821485774415055 0.2603434486654734 chr15 102531392 2278910 0.022226461140798712 0.23651914684986472 chr16 90354753 2319640 0.025672584152822597 0.4112570892445473 chr17 81195210 2121079 0.026123203573215712 0.26780684181240877 chr18 78077248 2054681 0.026316001813998364 0.36040553514529317 chr19 59128983 1496568 0.025310227304264646 0.41622240962747165 chr20 63025520 1683142 0.026705721745730937 0.2770989845219349 chr21 48129895 1021985 0.021233892157878177 0.24713594776764344 chr22 51304566 926651 0.01806176471700394 0.2277964596945316 chrMT 16571 6040 0.3644921851427192 0.9171169194804211 chrX 155270560 2445306 0.015748677663041853 0.21885195640379987 chrY 59373566 775443 0.01306040806105532 0.5267998107683836