BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926899.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 36,891,740 number of mapped reads = 34,693,324 (94.04%) number of supplementary alignments = 1,090,091 (2.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,404,390 number of mapped paired reads (second in pair) = 17,288,934 number of mapped paired reads (both in pair) = 34,160,462 number of mapped paired reads (singletons) = 532,862 number of mapped bases = 3,196,223,698 bp number of sequenced bases = 3,193,804,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,357,143 duplication rate = 7.65% >>>>>>> Insert size mean insert size = 297,846.412 std insert size = 5,384,169.1869 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 52.5684 >>>>>>> ACTG content number of A's = 908,094,778 bp (28.43%) number of C's = 638,257,041 bp (19.98%) number of T's = 916,559,712 bp (28.7%) number of G's = 730,684,922 bp (22.88%) number of N's = 207,988 bp (0.01%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 28,592,948 number of insertions = 524,971 mapped reads with insertion percentage = 1.49% number of deletions = 1,662,746 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.36% >>>>>>> Coverage mean coverageData = 1.0325X std coverageData = 4.0693X There is a 36.78% of reference with a coverageData >= 1X There is a 22.02% of reference with a coverageData >= 2X There is a 13.37% of reference with a coverageData >= 3X There is a 8.72% of reference with a coverageData >= 4X There is a 5.85% of reference with a coverageData >= 5X There is a 4.05% of reference with a coverageData >= 6X There is a 2.86% of reference with a coverageData >= 7X There is a 2.05% of reference with a coverageData >= 8X There is a 1.5% of reference with a coverageData >= 9X There is a 1.1% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.62% of reference with a coverageData >= 12X There is a 0.47% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 263756099 1.0581963565097798 3.2861429254881394 chr2 243199373 274913191 1.1304025483651226 6.479159994606285 chr3 198022430 218175667 1.101772496176317 2.275394642076026 chr4 191154276 186284287 0.9745232536676292 2.3436541937692947 chr5 180915260 189887143 1.0495916320160057 2.1136830250741037 chr6 171115067 182138493 1.064421130139288 2.536952137785042 chr7 159138663 163078538 1.0247574971771631 2.4973834353043793 chr8 146364022 160913245 1.0994043672836484 2.3804320413588735 chr9 141213431 136974716 0.9699836271239667 3.5599538903921175 chr10 135534747 162015025 1.1953763044985062 12.544186301422965 chr11 135006516 153286984 1.1354043385579997 2.5948768053898434 chr12 133851895 147911494 1.1050384755479181 2.508392294053977 chr13 115169878 95391654 0.8282691243278039 1.971064516568608 chr14 107349540 95056021 0.8854814002929123 2.063643597572582 chr15 102531392 97602305 0.9519260696275341 2.1817982691651254 chr16 90354753 101557098 1.1239818009352536 4.954019114894545 chr17 81195210 88477607 1.089689982943575 2.541583643234719 chr18 78077248 82164861 1.0523534461665451 3.437730916791821 chr19 59128983 54769348 0.9262690684194586 2.4321678970575764 chr20 63025520 77048506 1.2224969504416623 2.4798092528516484 chr21 48129895 38691355 0.8038944402434287 2.64278054999333 chr22 51304566 41159432 0.8022567036236112 2.0739736131336555 chrMT 16571 33826 2.0412769295757647 2.436952411075191 chrX 155270560 179375461 1.1552445035298384 2.3825194062172392 chrY 59373566 5561342 0.09366696957363146 2.496338944231311