BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124897.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,159,858 number of mapped reads = 2,141,086 (99.13%) number of supplementary alignments = 630,581 (29.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,072,046 number of mapped paired reads (second in pair) = 1,069,040 number of mapped paired reads (both in pair) = 2,132,358 number of mapped paired reads (singletons) = 8,728 number of mapped bases = 289,143,928 bp number of sequenced bases = 288,795,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 738,181 duplication rate = 23.55% >>>>>>> Insert size mean insert size = 1,366,629.152 std insert size = 11,027,432.0597 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 47.3709 >>>>>>> ACTG content number of A's = 83,520,986 bp (28.92%) number of C's = 60,522,124 bp (20.96%) number of T's = 83,472,584 bp (28.9%) number of G's = 61,255,523 bp (21.21%) number of N's = 23,863 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0178 number of mismatches = 4,860,985 number of insertions = 93,530 mapped reads with insertion percentage = 4.08% number of deletions = 170,740 mapped reads with deletion percentage = 7.58% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0934X std coverageData = 4.1715X There is a 4.52% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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% 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 22055683 0.08848797612424003 2.604566809287776 chr2 243199373 21130266 0.08688454143341891 2.7470028853413395 chr3 198022430 17793554 0.08985625517270948 1.3299925485108908 chr4 191154276 15731780 0.0822988652369984 2.0739298826337866 chr5 180915260 15981883 0.08833905442802338 0.4687928122720097 chr6 171115067 15482710 0.09048127830847298 1.4677200844471 chr7 159138663 14665186 0.09215350766142857 2.678663988268279 chr8 146364022 15264773 0.10429320533429998 0.8567930545159279 chr9 141213431 8941042 0.06331580457102554 2.9826119800730817 chr10 135534747 26491348 0.19545798097073955 17.353353336189727 chr11 135006516 10794441 0.07995496306267173 1.144439529971059 chr12 133851895 13860763 0.10355298294432067 0.4988036030600184 chr13 115169878 7437944 0.0645823728318962 0.3731362933013598 chr14 107349540 7575298 0.07056665543233813 0.459530408955229 chr15 102531392 7219518 0.07041275709979633 0.3923650189635305 chr16 90354753 14257558 0.15779532926176004 4.752095226481904 chr17 81195210 7513840 0.09254043434335597 3.3212904267856214 chr18 78077248 7460300 0.09555024275445774 2.6900582446781955 chr19 59128983 4193168 0.07091561172293459 1.4782165533083036 chr20 63025520 6866308 0.10894488454835438 0.8074313669466288 chr21 48129895 3453295 0.07174948127354111 1.3282453460782306 chr22 51304566 2057915 0.04011173196553305 0.3502900154841314 chrMT 16571 90744 5.476072657051476 4.606433327292352 chrX 155270560 20061139 0.12920117632086855 1.071370265140934 chrY 59373566 2763472 0.0465438104223014 4.556335879134878