BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472623.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,832,568 number of mapped reads = 18,706,399 (99.33%) number of supplementary alignments = 85,677 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,376,699 number of mapped paired reads (second in pair) = 9,329,700 number of mapped paired reads (both in pair) = 18,623,728 number of mapped paired reads (singletons) = 82,671 number of mapped bases = 1,840,304,568 bp number of sequenced bases = 1,840,024,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,863,246 duplication rate = 50.19% >>>>>>> Insert size mean insert size = 20,252.8867 std insert size = 1,424,340.8318 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.7605 >>>>>>> ACTG content number of A's = 486,969,803 bp (26.47%) number of C's = 434,936,954 bp (23.64%) number of T's = 487,789,228 bp (26.51%) number of G's = 429,983,545 bp (23.37%) number of N's = 345,333 bp (0.02%) GC percentage = 47.01% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 11,039,222 number of insertions = 105,708 mapped reads with insertion percentage = 0.56% number of deletions = 104,580 mapped reads with deletion percentage = 0.55% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.5945X std coverageData = 23.7914X There is a 3.78% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 328477285 1.3178594447714536 38.987258244393864 chr2 243199373 111457613 0.458297287633221 20.612999457489586 chr3 198022430 152211750 0.7686591362402734 26.154132378476334 chr4 191154276 36249774 0.1896362182345322 16.277077593348587 chr5 180915260 84163021 0.46520686535784767 20.6235117129921 chr6 171115067 100192915 0.5855294729832294 14.238012823901895 chr7 159138663 78795792 0.49513921076489126 16.91791317949223 chr8 146364022 71638812 0.48945643212783535 17.326891776437773 chr9 141213431 80547612 0.5703962535971525 16.77260081439756 chr10 135534747 41873755 0.30895217593168195 17.13184680588971 chr11 135006516 68256831 0.5055817528096199 23.43354928223625 chr12 133851895 77251014 0.5771379927045486 18.11648308702791 chr13 115169878 69224090 0.601060721797413 22.38474276001789 chr14 107349540 26400696 0.2459320831742735 9.667616261067607 chr15 102531392 28015575 0.27323899981773386 13.092006445608348 chr16 90354753 141748660 1.5688013667637384 60.887685495033324 chr17 81195210 57314533 0.7058856427614387 19.005684613189178 chr18 78077248 16303475 0.20881211130802152 8.259697411345327 chr19 59128983 60078014 1.0160501830379867 23.324272996300888 chr20 63025520 80307208 1.274201434593479 34.21103522956289 chr21 48129895 10988861 0.2283167457564576 10.980542653043862 chr22 51304566 19388350 0.37790690988400527 11.436485677448623 chrMT 16571 2096 0.1264860298111158 0.5167018142067137 chrX 155270560 94813176 0.6106320219364186 26.292687962362862 chrY 59373566 4603660 0.07753719896157155 8.365863527209457