BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695916.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 2,187,584 number of mapped reads = 2,180,236 (99.66%) number of supplementary alignments = 57,198 (2.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,091,410 number of mapped paired reads (second in pair) = 1,088,826 number of mapped paired reads (both in pair) = 2,176,120 number of mapped paired reads (singletons) = 4,116 number of mapped bases = 324,753,422 bp number of sequenced bases = 324,654,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,304 duplication rate = 0.25% >>>>>>> Insert size mean insert size = 71,295.5891 std insert size = 2,566,488.1493 median insert size = 309 >>>>>>> Mapping quality mean mapping quality = 54.746 >>>>>>> ACTG content number of A's = 95,769,655 bp (29.5%) number of C's = 66,387,399 bp (20.45%) number of T's = 95,126,745 bp (29.3%) number of G's = 67,327,178 bp (20.74%) number of N's = 43,858 bp (0.01%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,270,648 number of insertions = 38,209 mapped reads with insertion percentage = 1.69% number of deletions = 37,745 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.1049X std coverageData = 0.3545X There is a 9.5% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 26812000 0.10757044412739898 0.35969813958369273 chr2 243199373 28836749 0.11857246441174008 0.3984775026039191 chr3 198022430 23295881 0.11764263775573303 0.35623698605323434 chr4 191154276 23291887 0.1218486318349478 0.37259091160127794 chr5 180915260 20288167 0.1121418226411636 0.3473977589485163 chr6 171115067 21294515 0.12444558724919297 0.37352295344872766 chr7 159138663 16211897 0.10187277368291073 0.33456288532515166 chr8 146364022 14860542 0.10153138590301926 0.3312074711983429 chr9 141213431 13805522 0.09776351939214621 0.3434936390740928 chr10 135534747 15442611 0.11393839101643802 0.37547598745636823 chr11 135006516 16560433 0.12266395349391877 0.3696474384185595 chr12 133851895 15998650 0.11952501681055767 0.3607288371985892 chr13 115169878 11135714 0.09668946597303854 0.327221799223269 chr14 107349540 9770119 0.09101221113756053 0.3169110699429177 chr15 102531392 10246002 0.09993039009945363 0.3326311735779652 chr16 90354753 8160461 0.09031579113497216 0.3494837801881795 chr17 81195210 7687949 0.09468476034485286 0.33528502790143516 chr18 78077248 8990899 0.11515389220685647 0.3756289792575309 chr19 59128983 4596606 0.07773862777244114 0.29941820362789684 chr20 63025520 5778228 0.09168076677510952 0.31858094606102827 chr21 48129895 4398974 0.09139795547029554 0.36804533965196523 chr22 51304566 3282350 0.06397773640654128 0.27056941689231273 chrMT 16571 410325 24.761631766338784 8.13549578365274 chrX 155270560 11572334 0.07453012341811609 0.28277879901978353 chrY 59373566 2024607 0.034099467766514145 0.23209515129090044