BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046547.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,644,318 number of mapped reads = 9,606,031 (99.6%) number of supplementary alignments = 42,016 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,811,837 number of mapped paired reads (second in pair) = 4,794,194 number of mapped paired reads (both in pair) = 9,578,908 number of mapped paired reads (singletons) = 27,123 number of mapped bases = 949,165,881 bp number of sequenced bases = 948,851,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,157,014 duplication rate = 23.84% >>>>>>> Insert size mean insert size = 14,862.3466 std insert size = 1,296,667.6005 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 49.0657 >>>>>>> ACTG content number of A's = 253,747,565 bp (26.74%) number of C's = 220,231,075 bp (23.21%) number of T's = 255,160,596 bp (26.89%) number of G's = 219,629,932 bp (23.15%) number of N's = 82,369 bp (0.01%) GC percentage = 46.36% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 4,304,773 number of insertions = 57,459 mapped reads with insertion percentage = 0.59% number of deletions = 98,117 mapped reads with deletion percentage = 0.98% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.3066X std coverageData = 72.2685X There is a 1.45% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 86045701 0.3452175992773153 84.56947971754302 chr2 243199373 61415469 0.2525313624061029 66.19248370466414 chr3 198022430 13353991 0.06743675956304546 7.089032420261278 chr4 191154276 8314980 0.04349879152062494 6.210164527373382 chr5 180915260 237057192 1.3103217053110943 151.53654895987722 chr6 171115067 85617626 0.5003511818161518 86.85362283557988 chr7 159138663 19105572 0.12005612991734133 20.4243862737287 chr8 146364022 12742993 0.08706369793527538 22.077310791131904 chr9 141213431 6301822 0.0446262225581078 3.9779530901142097 chr10 135534747 8179647 0.06035092240958697 2.445626201481028 chr11 135006516 24611251 0.18229676410581547 33.01368831403858 chr12 133851895 63368734 0.47342425746008304 88.20930171227772 chr13 115169878 4971707 0.04316846632415466 14.959369693718982 chr14 107349540 4339927 0.04042799810786334 2.290331175851069 chr15 102531392 28396296 0.2769522138156478 44.36990920647768 chr16 90354753 229375705 2.5386124955706535 255.89056045717692 chr17 81195210 7567933 0.09320664359387702 8.954350147061428 chr18 78077248 1736464 0.02224033306091936 0.38837355159165565 chr19 59128983 10633923 0.1798428192143944 14.801342934148012 chr20 63025520 13711024 0.21754717771467813 11.740025913326882 chr21 48129895 467465 0.009712570534384088 0.2431777310212252 chr22 51304566 2184861 0.04258609262965016 1.9025731725932542 chrMT 16571 297262 17.93868806951904 7.77000638970699 chrX 155270560 19109721 0.1230736914969586 47.756571139254646 chrY 59373566 258615 0.004355726250297986 0.4407249546211919