BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506326.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 14,040,817 number of mapped reads = 9,221,932 (65.68%) number of supplementary alignments = 183,965 (1.31%) number of secondary alignments = 0 number of mapped bases = 738,310,622 bp number of sequenced bases = 738,000,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,894,282 duplication rate = 12.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.888 >>>>>>> ACTG content number of A's = 201,327,354 bp (27.28%) number of C's = 141,124,472 bp (19.12%) number of T's = 214,123,375 bp (29.01%) number of G's = 181,256,697 bp (24.56%) number of N's = 168,749 bp (0.02%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 5,551,416 number of insertions = 61,325 mapped reads with insertion percentage = 0.65% number of deletions = 149,761 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.2385X std coverageData = 1.6992X There is a 11.7% of reference with a coverageData >= 1X There is a 5.16% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 1.46% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 56765742 0.22774563919742452 3.1869746670378336 chr2 243199373 54753653 0.22513895625874003 1.7481222810008135 chr3 198022430 43968668 0.22203882661171262 0.8476481402539414 chr4 191154276 44223312 0.23134879807763234 1.4932364287401152 chr5 180915260 56606558 0.31288990215640183 1.0240456272030047 chr6 171115067 24646280 0.14403337141550487 0.7454255131221561 chr7 159138663 38619596 0.2426789019837373 2.0434828025382576 chr8 146364022 48412551 0.33076811048551263 2.3510514689008564 chr9 141213431 21411578 0.15162564812974483 1.5430243309066007 chr10 135534747 41517879 0.3063264581148331 2.1195942592458623 chr11 135006516 30358532 0.2248671612264996 1.3672526214029703 chr12 133851895 30634589 0.22886929617245988 0.9222152356033602 chr13 115169878 16084332 0.13965745452990755 0.6506854170365461 chr14 107349540 21750338 0.20261230742115896 0.960547875076453 chr15 102531392 26965066 0.2629932694174288 0.9527892345058223 chr16 90354753 27505163 0.3044130174314128 1.2660189167009541 chr17 81195210 18208898 0.22426074148955338 1.0808961967582722 chr18 78077248 13968369 0.17890447419458227 2.456951437086166 chr19 59128983 17756974 0.3003091394282902 2.3316796712958383 chr20 63025520 21031748 0.33370209400890305 1.1927067273100904 chr21 48129895 12829703 0.2665641177899931 1.4142937408903407 chr22 51304566 8788968 0.17130966471873088 0.801489531199673 chrMT 16571 92208 5.564419769476797 6.433415107417493 chrX 155270560 58231752 0.37503408244293057 1.2976668994965321 chrY 59373566 3178165 0.05352828226621928 2.076944024075146