BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438295.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 = 714,225,630 number of mapped reads = 711,676,393 (99.64%) number of supplementary alignments = 13,081,194 (1.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 356,151,408 number of mapped paired reads (second in pair) = 355,524,985 number of mapped paired reads (both in pair) = 709,817,614 number of mapped paired reads (singletons) = 1,858,779 number of mapped bases = 103,187,527,664 bp number of sequenced bases = 103,157,038,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 328,469,524 duplication rate = 43.19% >>>>>>> Insert size mean insert size = 49,154.5923 std insert size = 2,168,322.1905 median insert size = 270 >>>>>>> Mapping quality mean mapping quality = 54.9801 >>>>>>> ACTG content number of A's = 31,278,208,705 bp (30.32%) number of C's = 20,548,254,913 bp (19.92%) number of T's = 29,757,110,162 bp (28.85%) number of G's = 21,572,694,164 bp (20.91%) number of N's = 770,370 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 528,952,444 number of insertions = 13,385,348 mapped reads with insertion percentage = 1.85% number of deletions = 11,995,697 mapped reads with deletion percentage = 1.65% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 33.3326X std coverageData = 106.4936X There is a 88.12% of reference with a coverageData >= 1X There is a 87.15% of reference with a coverageData >= 2X There is a 86.13% of reference with a coverageData >= 3X There is a 85.11% of reference with a coverageData >= 4X There is a 83.99% of reference with a coverageData >= 5X There is a 82.8% of reference with a coverageData >= 6X There is a 81.53% of reference with a coverageData >= 7X There is a 80.19% of reference with a coverageData >= 8X There is a 78.78% of reference with a coverageData >= 9X There is a 77.31% of reference with a coverageData >= 10X There is a 75.78% of reference with a coverageData >= 11X There is a 74.21% of reference with a coverageData >= 12X There is a 72.6% of reference with a coverageData >= 13X There is a 70.96% of reference with a coverageData >= 14X There is a 69.3% of reference with a coverageData >= 15X There is a 67.62% of reference with a coverageData >= 16X There is a 65.93% of reference with a coverageData >= 17X There is a 64.24% of reference with a coverageData >= 18X There is a 62.54% of reference with a coverageData >= 19X There is a 60.85% of reference with a coverageData >= 20X There is a 59.17% of reference with a coverageData >= 21X There is a 57.51% of reference with a coverageData >= 22X There is a 55.86% of reference with a coverageData >= 23X There is a 54.23% of reference with a coverageData >= 24X There is a 52.62% of reference with a coverageData >= 25X There is a 51.03% of reference with a coverageData >= 26X There is a 49.48% of reference with a coverageData >= 27X There is a 47.95% of reference with a coverageData >= 28X There is a 46.45% of reference with a coverageData >= 29X There is a 44.98% of reference with a coverageData >= 30X There is a 43.54% of reference with a coverageData >= 31X There is a 42.14% of reference with a coverageData >= 32X There is a 40.77% of reference with a coverageData >= 33X There is a 39.43% of reference with a coverageData >= 34X There is a 38.13% of reference with a coverageData >= 35X There is a 36.86% of reference with a coverageData >= 36X There is a 35.63% of reference with a coverageData >= 37X There is a 34.43% of reference with a coverageData >= 38X There is a 33.26% of reference with a coverageData >= 39X There is a 32.13% of reference with a coverageData >= 40X There is a 31.03% of reference with a coverageData >= 41X There is a 29.96% of reference with a coverageData >= 42X There is a 28.93% of reference with a coverageData >= 43X There is a 27.93% of reference with a coverageData >= 44X There is a 26.96% of reference with a coverageData >= 45X There is a 26.02% of reference with a coverageData >= 46X There is a 25.11% of reference with a coverageData >= 47X There is a 24.23% of reference with a coverageData >= 48X There is a 23.38% of reference with a coverageData >= 49X There is a 22.56% of reference with a coverageData >= 50X There is a 21.76% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7898418717 31.688662139782593 34.80195683288707 chr2 243199373 8489731449 34.90852523291662 125.09079573975477 chr3 198022430 7764864633 39.21204599398159 31.21911407156357 chr4 191154276 7339719419 38.39683617121911 30.640457457283247 chr5 180915260 6535156101 36.122746643926 30.475168185768464 chr6 171115067 6335283018 37.02352533339452 33.071003785382665 chr7 159138663 6178604220 38.825286724948796 32.4536473757524 chr8 146364022 6173380668 42.17826610422061 33.278132472959534 chr9 141213431 4618651542 32.70688566443797 38.84545891267022 chr10 135534747 5233239105 38.61178938121307 41.0807974879857 chr11 135006516 4145950039 30.70925879607174 30.553593723345763 chr12 133851895 4442273719 33.18797779441225 29.461264736221608 chr13 115169878 3410023864 29.60864353785284 29.914863962172028 chr14 107349540 3011075008 28.049258599524507 30.52193363115241 chr15 102531392 3139785866 30.622678623147923 33.172436761434035 chr16 90354753 2531380215 28.01601610266147 44.672568138735656 chr17 81195210 2438344374 30.03064311306049 35.29080097013891 chr18 78077248 2711894241 34.73347627467607 31.833989896953497 chr19 59128983 1703516325 28.81017461436805 31.668708728255158 chr20 63025520 2339394280 37.11820672007149 34.27727676668874 chr21 48129895 1409358783 29.282398870805764 34.745909929027185 chr22 51304566 1102416383 21.48768557948624 30.860062701551172 chrMT 16571 634181730 38270.57691147185 15350.565059818846 chrX 155270560 3117915008 20.080529161484314 19.849308356571292 chrY 59373566 482968957 8.134410471488271 22.75636863101713