BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008703.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 = 1,177,825 number of mapped reads = 801,190 (68.02%) number of supplementary alignments = 4,101 (0.35%) number of secondary alignments = 0 number of mapped bases = 51,931,924 bp number of sequenced bases = 51,898,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,410 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7995 >>>>>>> ACTG content number of A's = 15,410,119 bp (29.69%) number of C's = 8,669,336 bp (16.7%) number of T's = 15,687,236 bp (30.23%) number of G's = 12,129,266 bp (23.37%) number of N's = 2,508 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 518,754 number of insertions = 4,328 mapped reads with insertion percentage = 0.54% number of deletions = 20,889 mapped reads with deletion percentage = 2.57% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.168X There is a 1.49% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 4181893 0.016777863915532633 0.19537721963607912 chr2 243199373 4738300 0.019483191677471964 0.22236546212670863 chr3 198022430 3836021 0.01937164895916084 0.1546911325651859 chr4 191154276 2704290 0.014147159334275107 0.1328524025123859 chr5 180915260 2642674 0.014607247614159248 0.13342823486422775 chr6 171115067 3038635 0.017757845952863987 0.1560470352255109 chr7 159138663 2894282 0.018187170518078312 0.20947363093528662 chr8 146364022 4506368 0.030788768567729028 0.2586874009678238 chr9 141213431 1725490 0.012219021857772155 0.13743092563304204 chr10 135534747 2572865 0.01898306564884059 0.1631511905511015 chr11 135006516 2480967 0.01837664635386932 0.17134713462304504 chr12 133851895 2380506 0.017784626807113936 0.14797927965941385 chr13 115169878 1471934 0.01278054666342531 0.12469908909449272 chr14 107349540 1860724 0.017333320664438805 0.1496683262386906 chr15 102531392 1580356 0.01541338676061279 0.13764988471772635 chr16 90354753 1222687 0.013532071743918109 0.13481822266417334 chr17 81195210 1346034 0.016577751323015238 0.14956772205115265 chr18 78077248 963740 0.012343416612224857 0.19566572803272198 chr19 59128983 856530 0.014485789481615132 0.14809968666082235 chr20 63025520 1083951 0.017198604628728173 0.14730231348846107 chr21 48129895 536371 0.011144237900373562 0.12055088502460765 chr22 51304566 559890 0.010913063761225463 0.11462807242849228 chrMT 16571 20696 1.2489288516082313 1.5599987574168268 chrX 155270560 2615794 0.016846683621157803 0.14865431893855988 chrY 59373566 110926 0.0018682724901515938 0.05262845403096778