BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472385.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,879,184 number of mapped reads = 19,676,877 (98.98%) number of supplementary alignments = 72,003 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,870,178 number of mapped paired reads (second in pair) = 9,806,699 number of mapped paired reads (both in pair) = 19,557,766 number of mapped paired reads (singletons) = 119,111 number of mapped bases = 1,926,655,284 bp number of sequenced bases = 1,926,418,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,641,914 duplication rate = 48.19% >>>>>>> Insert size mean insert size = 17,570.4107 std insert size = 1,317,246.4038 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 54.9713 >>>>>>> ACTG content number of A's = 517,984,543 bp (26.89%) number of C's = 447,122,107 bp (23.21%) number of T's = 518,743,537 bp (26.93%) number of G's = 442,330,915 bp (22.96%) number of N's = 237,775 bp (0.01%) GC percentage = 46.17% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,817,044 number of insertions = 107,076 mapped reads with insertion percentage = 0.54% number of deletions = 89,266 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.6224X std coverageData = 19.5399X There is a 5.25% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188419520 0.7559440343380328 24.621558989384727 chr2 243199373 159356511 0.6552505009953294 19.4000030383127 chr3 198022430 120124161 0.6066189623064417 15.152773948136003 chr4 191154276 45375813 0.23737796480158257 8.022932060229456 chr5 180915260 60337942 0.33351493953578043 11.799004816792452 chr6 171115067 158917873 0.9287193453280184 22.7218765418315 chr7 159138663 137248075 0.8624433083241374 22.77383781180953 chr8 146364022 90938089 0.6213144989962083 19.794819716043225 chr9 141213431 70337055 0.4980904047292782 13.813451642476856 chr10 135534747 31839298 0.23491612818667082 7.167352631956662 chr11 135006516 62502626 0.4629600692754711 17.500075020450993 chr12 133851895 108391725 0.8097884979514112 20.97250726471051 chr13 115169878 58294188 0.5061582855892233 15.44239924816416 chr14 107349540 33412039 0.3112452927138766 8.99728225851572 chr15 102531392 42437619 0.4138987891630302 10.438395698895391 chr16 90354753 129180191 1.4297000070378145 41.615124513653726 chr17 81195210 98869057 1.217671054733401 33.25986715367295 chr18 78077248 16919329 0.21669986370421251 5.799878276231742 chr19 59128983 38186298 0.6458135429117731 13.094367840683772 chr20 63025520 87132117 1.382489458238504 36.676510346882736 chr21 48129895 10767800 0.22372373760632555 9.537799229398088 chr22 51304566 28771003 0.5607883516644503 18.79419660244063 chrMT 16571 53154 3.207651922032466 2.3419178418644426 chrX 155270560 148342062 0.9553779029327903 22.699855451745943 chrY 59373566 501739 0.008450545146639836 0.6805573669810616