BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063554.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 = 2,759,908 number of mapped reads = 2,400,037 (86.96%) number of supplementary alignments = 20,288 (0.74%) number of secondary alignments = 0 number of mapped bases = 158,847,140 bp number of sequenced bases = 158,777,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,077 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6656 >>>>>>> ACTG content number of A's = 44,596,910 bp (28.09%) number of C's = 28,890,074 bp (18.2%) number of T's = 50,566,041 bp (31.85%) number of G's = 34,720,418 bp (21.87%) number of N's = 4,192 bp (0%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,292,081 number of insertions = 12,303 mapped reads with insertion percentage = 0.51% number of deletions = 42,393 mapped reads with deletion percentage = 1.75% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.538X There is a 4.1% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 18172239 0.07290749738994633 1.0919326829342388 chr2 243199373 14330504 0.05892492165265574 0.5996749332131205 chr3 198022430 9199021 0.04645443952990578 0.2587876886636341 chr4 191154276 10208576 0.05340490526092129 0.2895631335103661 chr5 180915260 6125139 0.03385639774113029 0.2204935977689251 chr6 171115067 12917502 0.07549014956117218 0.39010644778132303 chr7 159138663 12021925 0.07554370995312434 0.742432244601756 chr8 146364022 5936886 0.04056246828199351 0.9797180377766465 chr9 141213431 5732282 0.040593036791238366 0.43533628525226664 chr10 135534747 8004583 0.05905926839557977 0.4043137145497888 chr11 135006516 7976896 0.059085266669647266 0.40571598259951447 chr12 133851895 6307321 0.04712164142315654 0.2756263522612813 chr13 115169878 3249137 0.028211690907582625 0.20517523861371648 chr14 107349540 3161592 0.029451379111638486 0.25734315441397815 chr15 102531392 2832448 0.02762517844291044 0.21700782950257508 chr16 90354753 3341214 0.03697884050438387 0.2583737550797134 chr17 81195210 3837277 0.04725989377944832 0.2898678167200474 chr18 78077248 3975616 0.05091900780109463 0.7130153922205617 chr19 59128983 2721361 0.046024146906095104 0.7151167625131664 chr20 63025520 1850255 0.029357234974023223 0.22504128898044398 chr21 48129895 3040313 0.06316890988438682 0.3150807803897225 chr22 51304566 1620342 0.031582802980927666 0.2078675242273532 chrMT 16571 34611 2.0886488443666646 2.1782854444422077 chrX 155270560 11801785 0.07600787296703251 0.4032497650448925 chrY 59373566 448315 0.007550750783606294 0.16144049382225822