BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038460.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,337,776 number of mapped reads = 13,459,441 (93.87%) number of supplementary alignments = 233,010 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,856,035 number of mapped paired reads (second in pair) = 6,603,406 number of mapped paired reads (both in pair) = 13,116,064 number of mapped paired reads (singletons) = 343,377 number of mapped bases = 1,762,108,899 bp number of sequenced bases = 1,760,911,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,454,422 duplication rate = 18.22% >>>>>>> Insert size mean insert size = 75,356.9401 std insert size = 2,645,985.9031 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 52.862 >>>>>>> ACTG content number of A's = 509,404,196 bp (28.93%) number of C's = 337,349,849 bp (19.16%) number of T's = 523,282,625 bp (29.72%) number of G's = 390,745,210 bp (22.19%) number of N's = 129,665 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 23,288,242 number of insertions = 315,375 mapped reads with insertion percentage = 2.23% number of deletions = 602,383 mapped reads with deletion percentage = 4.32% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.5692X std coverageData = 8.6622X There is a 19.12% of reference with a coverageData >= 1X There is a 11.69% of reference with a coverageData >= 2X There is a 6.89% of reference with a coverageData >= 3X There is a 4.64% of reference with a coverageData >= 4X There is a 3.05% of reference with a coverageData >= 5X There is a 2.13% of reference with a coverageData >= 6X There is a 1.48% of reference with a coverageData >= 7X There is a 1.07% of reference with a coverageData >= 8X There is a 0.78% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% 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 151556904 0.60805025637228 10.655907685021132 chr2 243199373 163475291 0.6721863176842976 11.52670078968518 chr3 198022430 103834676 0.5243581547807489 1.687025929643526 chr4 191154276 81364049 0.4256459792717376 8.287992620099548 chr5 180915260 127724035 0.705988179217165 1.8973778905681744 chr6 171115067 109685192 0.641002536614733 8.055344405125274 chr7 159138663 88434758 0.5557088160279441 9.504851677129 chr8 146364022 115019361 0.7858444953090999 4.322896760383547 chr9 141213431 76812473 0.5439459437820755 13.907680166058778 chr10 135534747 95242837 0.7027189640159213 21.338559999007373 chr11 135006516 80529356 0.596484957807518 6.296611449687859 chr12 133851895 74164161 0.5540762870783413 1.7360178715042383 chr13 115169878 63092892 0.5478245969835966 1.6725139925951904 chr14 107349540 58225775 0.5423942664309507 1.7378218640726264 chr15 102531392 47425986 0.4625508839283095 1.4768142746622253 chr16 90354753 52427104 0.5802362605097265 7.86100185683839 chr17 81195210 39166256 0.48237150935381534 9.031725560513511 chr18 78077248 71023856 0.9096613651136884 11.768425598956343 chr19 59128983 21400215 0.36192428677489685 5.360277570052564 chr20 63025520 43246846 0.6861799156912946 3.2700542192546647 chr21 48129895 17398682 0.361494285412424 3.958582835271165 chr22 51304566 8354994 0.16285088543581092 1.0386231049259567 chrMT 16571 4770631 287.8903506125158 242.9797029894509 chrX 155270560 63902638 0.4115566917514821 2.0299573461178824 chrY 59373566 3829931 0.06450565896614666 8.412964275411992