BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472628.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 = 13,808,828 number of mapped reads = 13,692,460 (99.16%) number of supplementary alignments = 65,255 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,859,307 number of mapped paired reads (second in pair) = 6,833,153 number of mapped paired reads (both in pair) = 13,619,472 number of mapped paired reads (singletons) = 72,988 number of mapped bases = 1,345,619,731 bp number of sequenced bases = 1,345,447,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,971,645 duplication rate = 49.41% >>>>>>> Insert size mean insert size = 20,557.6168 std insert size = 1,448,036.1365 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.7243 >>>>>>> ACTG content number of A's = 356,013,161 bp (26.46%) number of C's = 318,377,115 bp (23.66%) number of T's = 356,220,561 bp (26.48%) number of G's = 314,589,568 bp (23.38%) number of N's = 246,785 bp (0.02%) GC percentage = 47.05% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,170,395 number of insertions = 76,164 mapped reads with insertion percentage = 0.55% number of deletions = 73,573 mapped reads with deletion percentage = 0.53% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 0.4347X std coverageData = 16.9038X There is a 2.95% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% 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 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187869849 0.7537387399327683 22.564333635580084 chr2 243199373 70134891 0.2883843413527222 9.88139821041169 chr3 198022430 130401111 0.658516871043346 21.076367406981152 chr4 191154276 22736930 0.11894544278988559 6.329317899335955 chr5 180915260 37839423 0.20915550739058716 11.342819909532924 chr6 171115067 119760153 0.699880817625487 26.123281239468117 chr7 159138663 70671534 0.44408777017310996 16.66872340769562 chr8 146364022 73071502 0.4992449715545532 16.959661492029714 chr9 141213431 62250162 0.44082323869037643 16.56044731741163 chr10 135534747 32237217 0.23785204689982561 8.836599655574544 chr11 135006516 29169218 0.21605785308910572 8.225186953535735 chr12 133851895 72592004 0.5423307903111868 16.050700091823426 chr13 115169878 62278399 0.5407524960649868 24.643441722985298 chr14 107349540 20394325 0.18998055324689794 7.952164468224137 chr15 102531392 17702446 0.17265391266705907 9.250505369700768 chr16 90354753 59775955 0.6615695690076204 18.676268539071394 chr17 81195210 67918506 0.8364841472791313 24.54161400279383 chr18 78077248 14103800 0.18063905121246077 6.446200113883909 chr19 59128983 52825197 0.8933892368823594 32.97454019727035 chr20 63025520 47683648 0.7565768279262115 20.459736722952904 chr21 48129895 10316492 0.21434686279702045 14.388332232656932 chr22 51304566 27746670 0.5408226238576894 22.141681417150714 chrMT 16571 3357 0.20258282541789874 0.579398568178209 chrX 155270560 55593642 0.3580436755042295 12.395998368043003 chrY 59373566 543300 0.009150536789385363 0.43020126649728385