BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618617.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 36,190,550 number of mapped reads = 32,520,089 (89.86%) number of supplementary alignments = 41,634 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,679,778 number of mapped paired reads (second in pair) = 15,840,311 number of mapped paired reads (both in pair) = 30,968,604 number of mapped paired reads (singletons) = 1,551,485 number of mapped bases = 3,081,659,063 bp number of sequenced bases = 3,079,856,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,951,420 duplication rate = 29.45% >>>>>>> Insert size mean insert size = 60,446.4436 std insert size = 2,521,639.5995 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.088 >>>>>>> ACTG content number of A's = 809,285,263 bp (26.28%) number of C's = 720,945,240 bp (23.41%) number of T's = 814,877,588 bp (26.46%) number of G's = 732,382,086 bp (23.78%) number of N's = 2,366,744 bp (0.08%) GC percentage = 47.19% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 45,175,939 number of insertions = 538,599 mapped reads with insertion percentage = 1.63% number of deletions = 1,286,180 mapped reads with deletion percentage = 3.87% homopolymer indels = 51.37% >>>>>>> Coverage mean coverageData = 0.9955X std coverageData = 4.9494X There is a 18.6% of reference with a coverageData >= 1X There is a 12.63% of reference with a coverageData >= 2X There is a 9.39% of reference with a coverageData >= 3X There is a 7.38% of reference with a coverageData >= 4X There is a 5.95% of reference with a coverageData >= 5X There is a 4.91% of reference with a coverageData >= 6X There is a 4.12% of reference with a coverageData >= 7X There is a 3.5% of reference with a coverageData >= 8X There is a 3% of reference with a coverageData >= 9X There is a 2.6% of reference with a coverageData >= 10X There is a 2.27% of reference with a coverageData >= 11X There is a 1.99% of reference with a coverageData >= 12X There is a 1.76% of reference with a coverageData >= 13X There is a 1.57% of reference with a coverageData >= 14X There is a 1.4% of reference with a coverageData >= 15X There is a 1.26% of reference with a coverageData >= 16X There is a 1.13% of reference with a coverageData >= 17X There is a 1.03% of reference with a coverageData >= 18X There is a 0.93% of reference with a coverageData >= 19X There is a 0.85% of reference with a coverageData >= 20X There is a 0.78% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.44% of reference with a coverageData >= 28X There is a 0.41% of reference with a coverageData >= 29X There is a 0.38% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.33% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% 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 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 297318295 1.1928487632534324 6.1312613999770305 chr2 243199373 263436702 1.0832129160135622 5.1167701227443 chr3 198022430 185007094 0.9342734254902336 4.382053195407057 chr4 191154276 148166848 0.7751165765185394 4.416534248641488 chr5 180915260 163631365 0.9044641397303909 4.079471987418647 chr6 171115067 159819874 0.933990657877018 4.309815749850579 chr7 159138663 151552565 0.952330264330548 4.679227189302571 chr8 146364022 156250432 1.0675467226501878 4.7383723239130955 chr9 141213431 140825018 0.9972494613490412 5.5864437537531835 chr10 135534747 169373598 1.2496691936865458 5.45545523122821 chr11 135006516 177716311 1.3163535825189356 5.6570457915667225 chr12 133851895 143530690 1.0723097345764137 5.104728216653512 chr13 115169878 83834658 0.7279217400924919 3.7333367840841576 chr14 107349540 93951745 0.8751946678113386 3.983709704927631 chr15 102531392 108601815 1.059205506543791 5.295854395253127 chr16 90354753 125067092 1.3841783397935912 6.29711199732089 chr17 81195210 123336420 1.5190110352568829 5.866891943377704 chr18 78077248 68952918 0.8831371464322103 4.135057412619462 chr19 59128983 78362768 1.3252852327935354 5.863899728367764 chr20 63025520 100041440 1.5873163759696072 6.2941229581913 chr21 48129895 39868021 0.8283421561588696 6.221897652467329 chr22 51304566 72039609 1.404155899106524 5.728116771563518 chrMT 16571 44355 2.6766640516565086 11.4062942945259 chrX 155270560 6604153 0.042533194959817236 1.975642237677202 chrY 59373566 24325277 0.409698770661678 2.8383306003592637