BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617732.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 35,073,224 number of mapped reads = 34,355,656 (97.95%) number of supplementary alignments = 1,351,817 (3.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,327,113 number of mapped paired reads (second in pair) = 17,028,543 number of mapped paired reads (both in pair) = 33,928,632 number of mapped paired reads (singletons) = 427,024 number of mapped bases = 4,511,795,780 bp number of sequenced bases = 4,508,188,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,633,522 duplication rate = 22.94% >>>>>>> Insert size mean insert size = 296,742.6138 std insert size = 5,278,936.1661 median insert size = 278 >>>>>>> Mapping quality mean mapping quality = 52.8711 >>>>>>> ACTG content number of A's = 1,324,422,456 bp (29.38%) number of C's = 840,338,134 bp (18.64%) number of T's = 1,358,884,287 bp (30.14%) number of G's = 984,376,646 bp (21.84%) number of N's = 166,559 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 55,328,004 number of insertions = 866,908 mapped reads with insertion percentage = 2.37% number of deletions = 1,861,018 mapped reads with deletion percentage = 5.19% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 1.4574X std coverageData = 15.339X There is a 35.31% of reference with a coverageData >= 1X There is a 24.37% of reference with a coverageData >= 2X There is a 17.36% of reference with a coverageData >= 3X There is a 12.9% of reference with a coverageData >= 4X There is a 9.72% of reference with a coverageData >= 5X There is a 7.47% of reference with a coverageData >= 6X There is a 5.8% of reference with a coverageData >= 7X There is a 4.56% of reference with a coverageData >= 8X There is a 3.62% of reference with a coverageData >= 9X There is a 2.9% of reference with a coverageData >= 10X There is a 2.34% of reference with a coverageData >= 11X There is a 1.9% of reference with a coverageData >= 12X There is a 1.55% of reference with a coverageData >= 13X There is a 1.28% of reference with a coverageData >= 14X There is a 1.06% of reference with a coverageData >= 15X There is a 0.88% of reference with a coverageData >= 16X There is a 0.73% of reference with a coverageData >= 17X There is a 0.62% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.44% of reference with a coverageData >= 20X There is a 0.38% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 337563207 1.3543124010912695 15.97290125347618 chr2 243199373 447091255 1.8383733867603351 21.18060979919185 chr3 198022430 472980754 2.3885211084421094 4.414324858136785 chr4 191154276 334110429 1.7478574688017965 16.928355710716787 chr5 180915260 207405495 1.14642344156043 3.372781549238011 chr6 171115067 263219282 1.538258942446021 11.903273827817346 chr7 159138663 233449677 1.4669576368126205 14.496476422109533 chr8 146364022 223824509 1.529231746583187 5.4123427886694 chr9 141213431 174372654 1.2348163539769812 28.05526560513687 chr10 135534747 224048786 1.6530726692543278 32.02732898220641 chr11 135006516 200963611 1.4885474935150538 10.340441189098145 chr12 133851895 208010352 1.5540336728142699 8.215262235589364 chr13 115169878 139329980 1.2097779594765221 2.9478202112590415 chr14 107349540 129982610 1.2108352769839534 3.372591932314792 chr15 102531392 61373848 0.5985859238115093 3.975772633142456 chr16 90354753 135994416 1.5051163495516389 21.583553558757032 chr17 81195210 86389699 1.0639753133220544 14.751891558159068 chr18 78077248 120067192 1.5378000003278804 23.65886796613849 chr19 59128983 57361339 0.9701052866070773 9.213398023162707 chr20 63025520 87496858 1.3882766536476019 5.797973988202594 chr21 48129895 57415378 1.1929254780215082 8.521464517398638 chr22 51304566 23419772 0.4564851401335312 2.596411760994456 chrMT 16571 1770639 106.85166857763564 58.62897158584175 chrX 155270560 265049453 1.7070167905622289 6.31792908957061 chrY 59373566 19104585 0.32176920281325194 23.9726100153074