BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124907.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,405,348 number of mapped reads = 2,358,451 (98.05%) number of supplementary alignments = 35,914 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,181,261 number of mapped paired reads (second in pair) = 1,177,190 number of mapped paired reads (both in pair) = 2,347,604 number of mapped paired reads (singletons) = 10,847 number of mapped bases = 315,324,421 bp number of sequenced bases = 315,079,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 388,710 duplication rate = 15.21% >>>>>>> Insert size mean insert size = 68,119.4987 std insert size = 2,461,136.9135 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.5216 >>>>>>> ACTG content number of A's = 93,475,797 bp (29.67%) number of C's = 62,792,380 bp (19.93%) number of T's = 93,339,057 bp (29.62%) number of G's = 65,441,348 bp (20.77%) number of N's = 30,627 bp (0.01%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 3,623,363 number of insertions = 68,187 mapped reads with insertion percentage = 2.72% number of deletions = 116,593 mapped reads with deletion percentage = 4.74% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.1019X std coverageData = 1.4319X There is a 5.7% of reference with a coverageData >= 1X There is a 3.16% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% 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 27770923 0.11141766824324181 1.6747435448250358 chr2 243199373 27044102 0.11120136399364812 1.4735777064846716 chr3 198022430 34533751 0.17439312809160054 0.5996850597962523 chr4 191154276 20188773 0.1056150739730248 1.3541741490034402 chr5 180915260 16975257 0.0938298792484393 0.42953059015327544 chr6 171115067 13652141 0.07978339511154794 0.715595506074237 chr7 159138663 21358709 0.13421445547773642 2.493962046748012 chr8 146364022 19759315 0.13500117535715164 0.6218376171255241 chr9 141213431 12766617 0.09040653505543676 2.30132127129186 chr10 135534747 16364369 0.12073928909167478 3.2796915949099334 chr11 135006516 13611013 0.10081745239614953 1.0440393758949829 chr12 133851895 14766009 0.11031602503647782 0.4627318301781956 chr13 115169878 6815849 0.05918083025146558 0.3328395915845127 chr14 107349540 8184488 0.07624148179861787 0.4059356677918118 chr15 102531392 7750385 0.07559036163285485 0.3799636714778135 chr16 90354753 7587737 0.08397717605403669 1.4924734835217164 chr17 81195210 8263383 0.10177180402637052 1.1636110544190612 chr18 78077248 7449583 0.09541298125671642 2.0971822303525753 chr19 59128983 3637900 0.06152481939356204 0.9207759577870055 chr20 63025520 6020045 0.09551757764156488 0.6013471951714501 chr21 48129895 3821466 0.07939900970072758 0.7673644311435177 chr22 51304566 2375669 0.046305215796972145 0.30908454859110124 chrMT 16571 278214 16.789210065777564 9.88865369041488 chrX 155270560 10146961 0.06535019259285212 0.5027648207899457 chrY 59373566 4201762 0.07076822705915962 2.2307868719969406