BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237589.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 = 1,192,530 number of mapped reads = 849,648 (71.25%) number of supplementary alignments = 3,809 (0.32%) number of secondary alignments = 0 number of mapped bases = 53,235,337 bp number of sequenced bases = 53,202,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,572 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1628 >>>>>>> ACTG content number of A's = 14,548,493 bp (27.35%) number of C's = 9,128,934 bp (17.16%) number of T's = 16,627,466 bp (31.25%) number of G's = 12,802,221 bp (24.06%) number of N's = 95,510 bp (0.18%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 562,188 number of insertions = 4,790 mapped reads with insertion percentage = 0.56% number of deletions = 19,924 mapped reads with deletion percentage = 2.32% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1877X There is a 1.48% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.04% 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 4470209 0.017934595236173956 0.22672816404778623 chr2 243199373 4754678 0.019550535601093016 0.25014520390378603 chr3 198022430 3845505 0.0194195425235414 0.16545115546979935 chr4 191154276 3473382 0.018170569200345797 0.16048223300700393 chr5 180915260 3062271 0.016926548926829058 0.14864262479462176 chr6 171115067 2814165 0.016446038617978626 0.16291787254388282 chr7 159138663 3182472 0.019998106933951054 0.24717871414718218 chr8 146364022 2910555 0.019885727108537643 0.2036973719381771 chr9 141213431 2162505 0.015313734569624614 0.19439245450217899 chr10 135534747 2263716 0.01670210813172507 0.17461815770946787 chr11 135006516 2231399 0.01652808372597364 0.19057291012552027 chr12 133851895 3186635 0.023807171351589756 0.18766563320721583 chr13 115169878 1855381 0.01610995020764023 0.1503941238970055 chr14 107349540 1499607 0.013969384498526962 0.1464193179018278 chr15 102531392 1680732 0.016392364984179675 0.1530290291157252 chr16 90354753 1322470 0.014636418739366152 0.1514384108905368 chr17 81195210 1138228 0.014018413155160262 0.14072750844724613 chr18 78077248 1422454 0.018218546842224768 0.298572062330058 chr19 59128983 821356 0.013890920464503846 0.17162400592922422 chr20 63025520 1042473 0.01654049026489587 0.1518967466484021 chr21 48129895 637633 0.013248169355033914 0.1427054931315885 chr22 51304566 491177 0.00957374827028066 0.1144640652772144 chrMT 16571 40796 2.46189125580834 2.119075635075753 chrX 155270560 2753575 0.017734044367457683 0.15961161648487085 chrY 59373566 171963 0.0028962888973183792 0.07761295985861849