BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004057.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 = 1,944,485 number of mapped reads = 1,708,687 (87.87%) number of supplementary alignments = 12,295 (0.63%) number of secondary alignments = 0 number of mapped bases = 114,597,723 bp number of sequenced bases = 114,553,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,486 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9094 >>>>>>> ACTG content number of A's = 31,461,414 bp (27.46%) number of C's = 21,838,230 bp (19.06%) number of T's = 35,515,505 bp (31%) number of G's = 25,720,317 bp (22.45%) number of N's = 18,433 bp (0.02%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 947,985 number of insertions = 7,820 mapped reads with insertion percentage = 0.45% number of deletions = 25,165 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3139X There is a 3.08% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 9311441 0.037357744436672835 0.5099294539548327 chr2 243199373 8771521 0.036067202360756084 0.35657509719884384 chr3 198022430 7599037 0.038374627561130324 0.2254404844407138 chr4 191154276 7718164 0.04037662228387713 0.240098396716793 chr5 180915260 5166876 0.02855964720720629 0.1964248144074549 chr6 171115067 6973052 0.04075066048976272 0.25517470521168345 chr7 159138663 8049933 0.05058439506934905 0.5113724115929171 chr8 146364022 7741523 0.0528922538081114 0.3429597197067535 chr9 141213431 3474642 0.024605605680666453 0.2684457125399842 chr10 135534747 5994217 0.044226422616187124 0.30557400565507836 chr11 135006516 4720887 0.03496784555198802 0.2517019601548199 chr12 133851895 6035334 0.04508964180148514 0.25026258224339976 chr13 115169878 3424821 0.029737124493611083 0.20517209922301752 chr14 107349540 3444835 0.03208989065067256 0.2265369045437434 chr15 102531392 3911467 0.03814897002471204 0.2305567006544508 chr16 90354753 2560499 0.028338287859632574 0.21067885661363409 chr17 81195210 1933029 0.023807180251150282 0.18612535384780035 chr18 78077248 2762817 0.03538568623730181 0.505900429614095 chr19 59128983 1961504 0.0331733085955495 0.3743358496362724 chr20 63025520 2562865 0.040663924708594236 0.24365015179788196 chr21 48129895 966312 0.020077168254782188 0.17767718071809255 chr22 51304566 1385227 0.02700007246918335 0.19057746720535518 chrMT 16571 75888 4.579566712932231 3.441472726867673 chrX 155270560 7774840 0.05007285347589395 0.2803911832650694 chrY 59373566 276992 0.004665241093991222 0.093569440978222