BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975266.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,471,474 number of mapped reads = 5,342,573 (97.64%) number of supplementary alignments = 63,345 (1.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,687,228 number of mapped paired reads (second in pair) = 2,655,345 number of mapped paired reads (both in pair) = 5,295,368 number of mapped paired reads (singletons) = 47,205 number of mapped bases = 737,261,332 bp number of sequenced bases = 736,754,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 670,913 duplication rate = 9.68% >>>>>>> Insert size mean insert size = 44,827.8978 std insert size = 1,990,611.3182 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.5414 >>>>>>> ACTG content number of A's = 214,477,625 bp (29.11%) number of C's = 147,538,312 bp (20.03%) number of T's = 216,323,055 bp (29.36%) number of G's = 158,353,275 bp (21.49%) number of N's = 62,260 bp (0.01%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 8,533,689 number of insertions = 124,354 mapped reads with insertion percentage = 2.2% number of deletions = 266,459 mapped reads with deletion percentage = 4.8% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.2382X std coverageData = 3.0841X There is a 12.48% of reference with a coverageData >= 1X There is a 6.3% of reference with a coverageData >= 2X There is a 2.08% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 58812480 0.23595720549879792 3.320982955563147 chr2 243199373 65799276 0.2705569310822195 2.8541226459347375 chr3 198022430 36376712 0.18369995762601238 0.6776399216188527 chr4 191154276 28100354 0.14700353341821137 2.5293904839668233 chr5 180915260 44867576 0.2480032695970478 0.8056322572716117 chr6 171115067 43405346 0.2536617421305162 2.953764895524065 chr7 159138663 25696256 0.16147085513719567 1.9938472243569891 chr8 146364022 50283905 0.3435537252454022 1.336418226478463 chr9 141213431 31952091 0.22626807360838078 4.257884055903417 chr10 135534747 25542922 0.18846032154396541 9.573501665858448 chr11 135006516 35561805 0.26340806394855787 3.646095965215291 chr12 133851895 32548849 0.24317062526458816 0.7285276807817158 chr13 115169878 22299519 0.193622841208532 0.6456341539196225 chr14 107349540 21961229 0.20457683377124858 0.7080049166177774 chr15 102531392 21058459 0.20538547842986468 0.6783548604674922 chr16 90354753 17968827 0.1988697484458842 2.641537682357354 chr17 81195210 14112064 0.17380414435777677 1.791664552625949 chr18 78077248 20460325 0.2620523330945271 4.601385383716512 chr19 59128983 10395708 0.17581408427065284 1.9989837826250871 chr20 63025520 23795884 0.3775595028807378 1.2447831187708172 chr21 48129895 9876137 0.2051975596456215 1.2750736298594643 chr22 51304566 7297829 0.14224521458772305 0.5700003416412862 chrMT 16571 106286 6.413976223523022 4.040585776909715 chrX 155270560 86687647 0.5583006012215065 2.039008204930129 chrY 59373566 2293846 0.03863412886468702 2.067782946310763