Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I1 R1 154 26.6 2069536 90.2% 1866721 108.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,231,117 Δ1 bp coding (2606/2652 nt) glnE → glutamine synthetase adenylyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,231,1150G.100.0% 40.0 / NA 10coding (2604/2652 nt)glnEglutamine synthetase adenylyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (4/6);  total (4/6)

CGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCG  >  AM260479/1230987‑1231195
                                                                                                                                |                                                                                
cgcgATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACggtg                                                                               >  2:239953/1‑130 (MQ=255)
  cgATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAg                                                                           >  1:349126/1‑133 (MQ=255)
    aTGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAc                                                                        <  1:910148/134‑1 (MQ=255)
       ccgccgCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACgg                                                                                 >  1:145196/1‑123 (MQ=255)
       ccgccgCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACgg                                                                                 <  2:145196/123‑1 (MQ=255)
                                        gccgcAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCt                                    >  2:563666/1‑133 (MQ=255)
                                             aaGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAc                                                                        >  1:566038/1‑93 (MQ=255)
                                             aaGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAc                                                                        <  2:566038/93‑1 (MQ=255)
                                                       aaGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGCgggc                    <  1:360236/134‑2 (MQ=255)
                                                          gCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGCgggcaat                 <  1:902866/134‑5 (MQ=255)
                                                                        accgaccTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTgcg  <  1:563666/134‑1 (MQ=255)
                                                                                           aGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGgcgc                                              <  1:578359/72‑1 (MQ=255)
                                                                                           aGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGgcgc                                              >  2:578359/1‑72 (MQ=255)
                                                                                                                                |                                                                                
CGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCG  >  AM260479/1230987‑1231195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCTGTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCT  >  AM260479/1230974‑1231254
                                                                                                                                               |                                                                                                                                         
GCTGTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGT                                                                                                                                     >  GWNJ‑0478:712:GW2002102894th:2:1206:20110:32658/1‑149 (MQ=60)
 gctccgtctcgtgggctcggagatgtgtataagagacAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAC                                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:1210:3621:23712/113‑1 (MQ=60)
  tttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAC                                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:1215:4076:96927/78‑1 (MQ=60)
   GTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCT                                                                                                                                 >  GWNJ‑0478:712:GW2002102894th:2:1112:3847:39471/1‑150 (MQ=60)
   GTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAC                                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:1214:3282:47455/148‑1 (MQ=60)
   GTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTAC                                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:2203:8816:24446/148‑1 (MQ=60)
    ttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCT                                                                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:2103:19102:92791/79‑1 (MQ=60)
     GCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGG                                                                                                                               >  GWNJ‑0478:712:GW2002102894th:2:1111:6260:57552/1‑150 (MQ=60)
                GATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC                                                                                                                    <  GWNJ‑0478:712:GW2002102894th:2:2208:6764:97239/150‑1 (MQ=60)
                                         cgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGC                                                                                          <  GWNJ‑0478:712:GW2002102894th:2:2104:19621:24881/103‑1 (MQ=60)
                                           ATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCACctgtctcttatacacatctccgagccc                                                                                         >  GWNJ‑0478:712:GW2002102894th:2:2105:13268:40196/1‑123 (MQ=60)
                                                                   GAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTG                                                               <  GWNJ‑0478:712:GW2002102894th:2:1208:15380:3127/150‑1 (MQ=60)
                                                                      GGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGC                                                            <  GWNJ‑0478:712:GW2002102894th:2:2208:10703:52623/150‑1 (MQ=60)
                                                                          tttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGC                                                          <  GWNJ‑0478:712:GW2002102894th:2:2101:8238:87333/81‑1 (MQ=60)
                                                                                    GACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCT                                              <  GWNJ‑0478:712:GW2002102894th:2:2105:6258:24490/150‑1 (MQ=60)
                                                                                                                         gtataagagacaGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGG          <  GWNJ‑0478:712:GW2002102894th:2:1113:4232:59011/137‑1 (MQ=60)
                                                                                                                            GTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTG                                                                                              <  GWNJ‑0478:712:GW2002102894th:2:1116:10293:5639/63‑1 (MQ=60)
                                                                                                                                ATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGctgtctcttatacacatctccgagcccacgagacggagctacatctcg  >  GWNJ‑0478:712:GW2002102894th:2:1201:12669:94484/1‑102 (MQ=60)
                                                                                                                                ATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCT  >  GWNJ‑0478:712:GW2002102894th:2:2106:12577:95196/1‑150 (MQ=60)
                                                                                                                                               |                                                                                                                                         
GCTGTGCCAGGACCGCGATGCCGCCGCGCTGCGCGACGAGATCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCT  >  AM260479/1230974‑1231254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑