BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237252.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,844,093 number of mapped reads = 2,577,986 (90.64%) number of supplementary alignments = 15,666 (0.55%) number of secondary alignments = 0 number of mapped bases = 174,964,993 bp number of sequenced bases = 174,891,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,496 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1228 >>>>>>> ACTG content number of A's = 49,824,376 bp (28.49%) number of C's = 31,923,742 bp (18.25%) number of T's = 55,188,778 bp (31.56%) number of G's = 37,952,048 bp (21.7%) number of N's = 2,945 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,410,426 number of insertions = 15,219 mapped reads with insertion percentage = 0.59% number of deletions = 43,922 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.6187X There is a 4.71% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15847151 0.06357918362016839 0.7776044133905504 chr2 243199373 11652778 0.047914506753271933 0.8032844515656358 chr3 198022430 17856472 0.09017398685593345 0.34813543342151926 chr4 191154276 7582346 0.03966610718140566 0.323737425730222 chr5 180915260 12175110 0.06729730814304996 0.30631555558009005 chr6 171115067 18522221 0.10824424362350278 0.8533764841960405 chr7 159138663 9341826 0.05870242858581764 0.932207391690161 chr8 146364022 10581035 0.07229259523901305 1.116900474510083 chr9 141213431 8945108 0.06334459786619022 0.7306553197838747 chr10 135534747 8046200 0.05936632618645018 0.5516555563281381 chr11 135006516 4703209 0.03483690372396544 0.42946133291456956 chr12 133851895 4478700 0.033460116496669697 0.2575101594897103 chr13 115169878 5876196 0.05102198684277498 0.2583095202012565 chr14 107349540 3146602 0.029311741810910414 0.3412519273110515 chr15 102531392 3740807 0.036484504179949105 0.2335193226831309 chr16 90354753 4941265 0.05468738318613964 0.3608076256341091 chr17 81195210 4714104 0.05805889288296687 0.3870056751887159 chr18 78077248 7297466 0.09346469281294341 1.1894958389154242 chr19 59128983 1553812 0.02627834813259007 0.6267675070519558 chr20 63025520 2274510 0.036088714539761035 0.25490297341306456 chr21 48129895 2959439 0.061488582096428844 0.39476117049546805 chr22 51304566 1037881 0.020229797870232446 0.15684660236024936 chrMT 16571 113298 6.837125098062881 5.03549451749368 chrX 155270560 7172137 0.04619122259879787 0.34555409530998166 chrY 59373566 405320 0.006826606978600544 0.2270539236956996