BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438275.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 = 1,018,290,224 number of mapped reads = 1,014,020,573 (99.58%) number of supplementary alignments = 12,041,453 (1.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 507,336,618 number of mapped paired reads (second in pair) = 506,683,955 number of mapped paired reads (both in pair) = 1,011,970,618 number of mapped paired reads (singletons) = 2,049,955 number of mapped bases = 111,339,634,337 bp number of sequenced bases = 111,313,021,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 419,315,114 duplication rate = 41.35% >>>>>>> Insert size mean insert size = 90,028.6059 std insert size = 3,131,405.42 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.0844 >>>>>>> ACTG content number of A's = 33,813,235,207 bp (30.38%) number of C's = 22,048,259,577 bp (19.81%) number of T's = 33,007,992,930 bp (29.65%) number of G's = 22,443,239,153 bp (20.16%) number of N's = 294,544 bp (0%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 337,359,124 number of insertions = 15,410,032 mapped reads with insertion percentage = 1.5% number of deletions = 11,262,586 mapped reads with deletion percentage = 1.1% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 35.966X std coverageData = 460.0129X There is a 88.94% of reference with a coverageData >= 1X There is a 87.76% of reference with a coverageData >= 2X There is a 85.8% of reference with a coverageData >= 3X There is a 84.25% of reference with a coverageData >= 4X There is a 82.42% of reference with a coverageData >= 5X There is a 80.7% of reference with a coverageData >= 6X There is a 78.87% of reference with a coverageData >= 7X There is a 77.07% of reference with a coverageData >= 8X There is a 75.24% of reference with a coverageData >= 9X There is a 73.41% of reference with a coverageData >= 10X There is a 71.58% of reference with a coverageData >= 11X There is a 69.76% of reference with a coverageData >= 12X There is a 67.94% of reference with a coverageData >= 13X There is a 66.15% of reference with a coverageData >= 14X There is a 64.38% of reference with a coverageData >= 15X There is a 62.63% of reference with a coverageData >= 16X There is a 60.92% of reference with a coverageData >= 17X There is a 59.23% of reference with a coverageData >= 18X There is a 57.57% of reference with a coverageData >= 19X There is a 55.96% of reference with a coverageData >= 20X There is a 54.37% of reference with a coverageData >= 21X There is a 52.83% of reference with a coverageData >= 22X There is a 51.32% of reference with a coverageData >= 23X There is a 49.85% of reference with a coverageData >= 24X There is a 48.42% of reference with a coverageData >= 25X There is a 47.03% of reference with a coverageData >= 26X There is a 45.68% of reference with a coverageData >= 27X There is a 44.36% of reference with a coverageData >= 28X There is a 43.08% of reference with a coverageData >= 29X There is a 41.85% of reference with a coverageData >= 30X There is a 40.64% of reference with a coverageData >= 31X There is a 39.48% of reference with a coverageData >= 32X There is a 38.35% of reference with a coverageData >= 33X There is a 37.25% of reference with a coverageData >= 34X There is a 36.19% of reference with a coverageData >= 35X There is a 35.16% of reference with a coverageData >= 36X There is a 34.16% of reference with a coverageData >= 37X There is a 33.19% of reference with a coverageData >= 38X There is a 32.25% of reference with a coverageData >= 39X There is a 31.34% of reference with a coverageData >= 40X There is a 30.46% of reference with a coverageData >= 41X There is a 29.61% of reference with a coverageData >= 42X There is a 28.78% of reference with a coverageData >= 43X There is a 27.98% of reference with a coverageData >= 44X There is a 27.21% of reference with a coverageData >= 45X There is a 26.46% of reference with a coverageData >= 46X There is a 25.73% of reference with a coverageData >= 47X There is a 25.03% of reference with a coverageData >= 48X There is a 24.35% of reference with a coverageData >= 49X There is a 23.69% of reference with a coverageData >= 50X There is a 23.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9062202331 36.35779238840893 46.017549035336145 chr2 243199373 9959111834 40.95040094531823 1634.6293636914413 chr3 198022430 8175257972 41.28450485129387 42.235680086257574 chr4 191154276 8431198075 44.10677203475166 43.99120952901986 chr5 180915260 7137430261 39.451786770226015 41.29956657894267 chr6 171115067 6800212387 39.740582207176416 41.70578301861492 chr7 159138663 6244736141 39.240848347456584 44.331583096059916 chr8 146364022 6043800683 41.292939346802044 43.110187426089375 chr9 141213431 4522265307 32.024328528636914 41.89907152845445 chr10 135534747 4830213711 35.63819476491884 41.71700192771847 chr11 135006516 5033208736 37.28122823345801 43.070753460668996 chr12 133851895 5185460189 38.74028222760686 44.233896275995455 chr13 115169878 3884162563 33.72550731537633 39.73965387302646 chr14 107349540 3237724828 30.160584088203823 39.69577550403939 chr15 102531392 2947849213 28.75069922975395 40.34450053378737 chr16 90354753 2019803098 22.35414331772895 31.149648776261525 chr17 81195210 1824180925 22.46660763609085 31.033972271411756 chr18 78077248 2943023352 37.69373828339851 39.78204940167988 chr19 59128983 914154824 15.460350873952965 24.15212043532911 chr20 63025520 1714258142 27.19942877107559 36.29733069840563 chr21 48129895 1174786448 24.408664261577965 35.041110559681 chr22 51304566 592986486 11.558162016222884 23.827314047725828 chrMT 16571 23522 1.4194677448554704 3.4725124445693005 chrX 155270560 8578900580 55.25130185657861 58.06390146424692 chrY 59373566 82682729 1.392584858386306 8.327243956287713