BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068959.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 = 2,120,864 number of mapped reads = 1,589,896 (74.96%) number of supplementary alignments = 9,270 (0.44%) number of secondary alignments = 0 number of mapped bases = 102,610,934 bp number of sequenced bases = 102,560,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,451 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8455 >>>>>>> ACTG content number of A's = 26,799,227 bp (26.13%) number of C's = 17,929,809 bp (17.48%) number of T's = 33,447,970 bp (32.61%) number of G's = 24,143,308 bp (23.54%) number of N's = 239,798 bp (0.23%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,009,666 number of insertions = 10,144 mapped reads with insertion percentage = 0.63% number of deletions = 30,533 mapped reads with deletion percentage = 1.9% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.3506X There is a 2.99% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 11138055 0.044686167502066124 0.651872313029079 chr2 243199373 7754724 0.03188628286471775 0.3380196845832458 chr3 198022430 5729146 0.028931803331572085 0.1966901275769995 chr4 191154276 6160922 0.032230102977136646 0.21256072026017317 chr5 180915260 3805661 0.021035599760904636 0.16097437790195757 chr6 171115067 8497094 0.04965719354216774 0.31562308013712737 chr7 159138663 5355410 0.03365247576574148 0.4798356971771578 chr8 146364022 5973217 0.04081069185158085 0.46488090838594426 chr9 141213431 4819474 0.03412900576008241 0.35620703391719644 chr10 135534747 6916056 0.051027918324147534 0.4846860447387324 chr11 135006516 3774870 0.027960650432605785 0.30929989183337014 chr12 133851895 6334360 0.047323648275581005 0.23809312461528628 chr13 115169878 2174005 0.018876506928313323 0.1468473537116427 chr14 107349540 2128406 0.019826875830115342 0.18425735085380618 chr15 102531392 2169909 0.021163362338823998 0.15704860399836665 chr16 90354753 2008613 0.02223029706029964 0.19201394677137604 chr17 81195210 2870224 0.03534967148924179 0.22470277490380813 chr18 78077248 2267208 0.02903801117580374 0.5751872880955854 chr19 59128983 1541452 0.026069313588566203 0.41707642768334713 chr20 63025520 1147483 0.018206640738545277 0.16045108135203642 chr21 48129895 1332947 0.027694783044924575 0.19607231657984564 chr22 51304566 1055575 0.020574679454456353 0.1537021345955162 chrMT 16571 47422 2.861746424476495 2.3575907241306964 chrX 155270560 7316162 0.047118797021148115 0.279442492561654 chrY 59373566 292539 0.004927091628621397 0.11292738281161821