BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438255.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 653,579,140 number of mapped reads = 651,418,446 (99.67%) number of supplementary alignments = 11,420,108 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 325,914,479 number of mapped paired reads (second in pair) = 325,503,967 number of mapped paired reads (both in pair) = 649,863,308 number of mapped paired reads (singletons) = 1,555,138 number of mapped bases = 94,118,720,258 bp number of sequenced bases = 94,091,667,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 261,415,149 duplication rate = 37.39% >>>>>>> Insert size mean insert size = 40,002.9221 std insert size = 1,938,583.108 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 55.0574 >>>>>>> ACTG content number of A's = 28,502,519,728 bp (30.29%) number of C's = 18,772,292,148 bp (19.95%) number of T's = 27,137,773,893 bp (28.84%) number of G's = 19,678,377,220 bp (20.91%) number of N's = 704,329 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 482,475,905 number of insertions = 12,051,304 mapped reads with insertion percentage = 1.82% number of deletions = 10,691,375 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 30.4031X std coverageData = 82.4403X There is a 91.1% of reference with a coverageData >= 1X There is a 90.31% of reference with a coverageData >= 2X There is a 89.38% of reference with a coverageData >= 3X There is a 88.37% of reference with a coverageData >= 4X There is a 87.21% of reference with a coverageData >= 5X There is a 85.94% of reference with a coverageData >= 6X There is a 84.54% of reference with a coverageData >= 7X There is a 83.04% of reference with a coverageData >= 8X There is a 81.44% of reference with a coverageData >= 9X There is a 79.74% of reference with a coverageData >= 10X There is a 77.96% of reference with a coverageData >= 11X There is a 76.11% of reference with a coverageData >= 12X There is a 74.2% of reference with a coverageData >= 13X There is a 72.24% of reference with a coverageData >= 14X There is a 70.25% of reference with a coverageData >= 15X There is a 68.23% of reference with a coverageData >= 16X There is a 66.19% of reference with a coverageData >= 17X There is a 64.15% of reference with a coverageData >= 18X There is a 62.11% of reference with a coverageData >= 19X There is a 60.08% of reference with a coverageData >= 20X There is a 58.06% of reference with a coverageData >= 21X There is a 56.06% of reference with a coverageData >= 22X There is a 54.09% of reference with a coverageData >= 23X There is a 52.15% of reference with a coverageData >= 24X There is a 50.24% of reference with a coverageData >= 25X There is a 48.38% of reference with a coverageData >= 26X There is a 46.56% of reference with a coverageData >= 27X There is a 44.78% of reference with a coverageData >= 28X There is a 43.05% of reference with a coverageData >= 29X There is a 41.37% of reference with a coverageData >= 30X There is a 39.73% of reference with a coverageData >= 31X There is a 38.15% of reference with a coverageData >= 32X There is a 36.61% of reference with a coverageData >= 33X There is a 35.13% of reference with a coverageData >= 34X There is a 33.7% of reference with a coverageData >= 35X There is a 32.31% of reference with a coverageData >= 36X There is a 30.98% of reference with a coverageData >= 37X There is a 29.69% of reference with a coverageData >= 38X There is a 28.46% of reference with a coverageData >= 39X There is a 27.26% of reference with a coverageData >= 40X There is a 26.12% of reference with a coverageData >= 41X There is a 25.02% of reference with a coverageData >= 42X There is a 23.96% of reference with a coverageData >= 43X There is a 22.94% of reference with a coverageData >= 44X There is a 21.97% of reference with a coverageData >= 45X There is a 21.04% of reference with a coverageData >= 46X There is a 20.14% of reference with a coverageData >= 47X There is a 19.28% of reference with a coverageData >= 48X There is a 18.46% of reference with a coverageData >= 49X There is a 17.67% of reference with a coverageData >= 50X There is a 16.92% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7622368467 30.58114132843023 30.976223906078165 chr2 243199373 8407815556 34.571699146609234 94.47941293664 chr3 198022430 6901887260 34.85406809723525 91.32040267115822 chr4 191154276 6401801628 33.490235018336705 27.521804695567447 chr5 180915260 6150655170 33.997437087396605 28.208556659532153 chr6 171115067 5996746487 35.0451108259216 28.5546833353911 chr7 159138663 4929226892 30.9744143822548 25.59396936083531 chr8 146364022 5008225738 34.21760122169914 27.39375659964724 chr9 141213431 3927653610 27.813598056405837 32.494176712619684 chr10 135534747 4118006604 30.38340126904874 39.28318051659687 chr11 135006516 4345108094 32.184432446208746 27.54462852001698 chr12 133851895 4278197862 31.962176269525358 26.23339990302485 chr13 115169878 3305274496 28.6991230120084 26.99042726865283 chr14 107349540 3142824304 29.2765511990084 29.8749874329627 chr15 102531392 2673454994 26.074502080299467 26.744111900371003 chr16 90354753 2579768314 28.551550730264296 46.78243266097003 chr17 81195210 2343049241 28.856988497227853 33.95164997341206 chr18 78077248 2564559781 32.84644178288661 27.851968552999015 chr19 59128983 1405503440 23.770127079642144 112.22507396972726 chr20 63025520 2001321750 31.754148954264874 29.154367807608548 chr21 48129895 1279189605 26.57785987274645 48.65045914195197 chr22 51304566 996134523 19.416098812725558 26.28088666862302 chrMT 16571 450665478 27196.033914670206 10442.88774881772 chrX 155270560 2839016463 18.284319081479453 20.986312708924107 chrY 59373566 450264501 7.583585277663801 26.447309020766767