BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004018.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 = 3,010,153 number of mapped reads = 2,096,292 (69.64%) number of supplementary alignments = 12,805 (0.43%) number of secondary alignments = 0 number of mapped bases = 125,185,319 bp number of sequenced bases = 125,124,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 588,463 duplication rate = 17.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0375 >>>>>>> ACTG content number of A's = 34,224,545 bp (27.35%) number of C's = 22,198,320 bp (17.74%) number of T's = 41,546,994 bp (33.2%) number of G's = 27,132,262 bp (21.68%) number of N's = 22,488 bp (0.02%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 1,360,197 number of insertions = 11,700 mapped reads with insertion percentage = 0.55% number of deletions = 38,278 mapped reads with deletion percentage = 1.8% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.797X There is a 1.44% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 10050589 0.040323225513648774 0.5666699715579998 chr2 243199373 10421600 0.042852084162240005 0.8880354888743888 chr3 198022430 8939668 0.04514472426179196 0.5677140970969837 chr4 191154276 9390636 0.04912595311234366 0.5779193647922396 chr5 180915260 7310872 0.04041047725880061 0.4928615980850643 chr6 171115067 7321909 0.042789388032089544 0.8571788891990562 chr7 159138663 7631440 0.047954657002490964 0.8361176101193444 chr8 146364022 6666294 0.045545988070756896 0.7245478852023233 chr9 141213431 4963910 0.03515182631601097 0.47179844959985207 chr10 135534747 5252488 0.03875381122746332 0.5167875980945985 chr11 135006516 5581024 0.041338923226490784 0.4955972540444569 chr12 133851895 5319806 0.03974397224633988 0.5870930040887307 chr13 115169878 4049448 0.03516065198922934 0.7758085774699863 chr14 107349540 3757953 0.03500669867798222 0.459163823230174 chr15 102531392 3144839 0.03067196239762355 0.4653827264069274 chr16 90354753 3551643 0.03930776060004281 0.513403579765837 chr17 81195210 3022310 0.037222762278710776 0.45222223552862917 chr18 78077248 3717070 0.0476075949808067 3.221976934699206 chr19 59128983 2258413 0.038194687028525416 0.5104826932817538 chr20 63025520 2526662 0.040089506599866216 0.5100875616762147 chr21 48129895 1822092 0.03785780126883718 0.46546072381610876 chr22 51304566 1351724 0.026347050669915033 0.36083124888040713 chrMT 16571 125021 7.544565807736407 7.976791408049662 chrX 155270560 6538806 0.042112336041037014 0.5199639015666608 chrY 59373566 469102 0.007900856081307294 0.26298404714466905