BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234096.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 = 3,956,514 number of mapped reads = 3,746,057 (94.68%) number of supplementary alignments = 19,277 (0.49%) number of secondary alignments = 0 number of mapped bases = 239,766,084 bp number of sequenced bases = 239,662,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 400,183 duplication rate = 8.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8605 >>>>>>> ACTG content number of A's = 60,023,529 bp (25.05%) number of C's = 43,381,060 bp (18.1%) number of T's = 78,540,506 bp (32.77%) number of G's = 57,695,208 bp (24.07%) number of N's = 22,396 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,319,707 number of insertions = 15,660 mapped reads with insertion percentage = 0.41% number of deletions = 58,197 mapped reads with deletion percentage = 1.54% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 0.0775X std coverageData = 0.8266X There is a 5.97% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 20311934 0.08149200960265611 1.7536992585894726 chr2 243199373 15356761 0.0631447392752941 1.4969436364068747 chr3 198022430 22405319 0.11314535934136351 0.4228824146088526 chr4 191154276 9804679 0.05129196795995293 0.3070409404786492 chr5 180915260 19423390 0.10736181127009407 0.4167573095927442 chr6 171115067 17029685 0.09952183228844483 0.6441244782060439 chr7 159138663 13245536 0.08323267112027956 1.0247735555671802 chr8 146364022 9459111 0.0646272961807513 0.5612605876737216 chr9 141213431 11117705 0.07872979872573169 0.5044914361496029 chr10 135534747 10373697 0.07653902212987493 0.598127291476865 chr11 135006516 13082419 0.09690213026458663 0.5452294958829543 chr12 133851895 7559741 0.056478400996862986 0.31399344894576653 chr13 115169878 8448540 0.07335720195865797 0.3929453219267896 chr14 107349540 12655740 0.11789282003444077 0.4533416522045434 chr15 102531392 2791474 0.02722555449164291 0.25853965997856965 chr16 90354753 6427751 0.071139046774883 0.386383948266252 chr17 81195210 6285205 0.07740856880596775 0.3820301961694492 chr18 78077248 4042671 0.0517778367393277 1.2004321807281113 chr19 59128983 8454314 0.14298087961364056 1.0462224804330482 chr20 63025520 6019558 0.09550985061289459 0.40673493932183263 chr21 48129895 4392449 0.09126238484418052 0.3968110677365316 chr22 51304566 2635209 0.05136402479264711 0.278091077901466 chrMT 16571 166549 10.050630619757408 6.015473545028994 chrX 155270560 7753400 0.04993477192328024 0.34485679574363176 chrY 59373566 523247 0.008812793895519094 0.21193940388908397