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
A2 F2 I1 R1 13 29.1 961540 98.8% 950001 141.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,404,859 C→T A72T (GCC→ACC)  nuoA ← NADH:ubiquinone oxidoreductase, membrane subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,404,8590CT100.0% 86.8 / NA 26A72T (GCC→ACC) nuoANADH:ubiquinone oxidoreductase, membrane subunit A
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/11);  total (15/11)

AATACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGCCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATG  >  NC_000913/2404713‑2405004
                                                                                                                                                  |                                                                                                                                                 
aaTACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGtca                                                                                                                                                 <  1:30909/149‑1 (MQ=255)
   aCGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGtcac                                                                                                                                                >  8:66583/1‑147 (MQ=255)
     gCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGtcac                                                                                                                                                >  5:61140/1‑145 (MQ=255)
      cACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGa                                                                                                                                            >  1:67705/1‑148 (MQ=255)
          aGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATaaaa                                                                                                                                       <  6:48379/149‑1 (MQ=255)
                       cTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGCCCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAgg                                                                                                                          >  8:80928/1‑149 (MQ=255)
                          ccAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCg                                                                                                                        <  7:80928/148‑1 (MQ=255)
                                     aaaataaaaatTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGa                                                                                                            <  6:61140/149‑1 (MQ=255)
                                                        ccACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATAcc                                                                                          <  7:66583/148‑1 (MQ=255)
                                                          acaAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGTCGACCGAGTCGATACCGGa                                                                                       >  2:55102/1‑149 (MQ=255)
                                                                   aCCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGAc                                                                                                                             <  2:7343/102‑1 (MQ=255)
                                                                   aCCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGAc                                                                                                                             >  1:7343/1‑102 (MQ=255)
                                                                     ccAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCa                                                                            >  6:7523/1‑149 (MQ=255)
                                                                                      tAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTcgcg                                                           >  2:96676/1‑149 (MQ=255)
                                                                                         agGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGt                                                        >  1:88897/1‑149 (MQ=255)
                                                                                         agGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGt                                                        >  5:31509/1‑149 (MQ=255)
                                                                                                  aTGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCg                                               >  1:126710/1‑149 (MQ=255)
                                                                                                   tgagAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGACGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCAGCCGc                                              >  6:106207/4‑149 (MQ=255)
                                                                                                             tACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAaacca                                    <  2:117304/149‑1 (MQ=255)
                                                                                                              aCAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAaaccaa                                   >  3:73386/1‑149 (MQ=255)
                                                                                                                aGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAaaccaacc                                 >  6:119061/1‑149 (MQ=255)
                                                                                                                          cGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGc                       <  2:88897/149‑1 (MQ=255)
                                                                                                                            tCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAAACAACCGCCTACCAGCAt                     >  2:72245/1‑149 (MQ=255)
                                                                                                                                aGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAgg                 <  2:126710/149‑1 (MQ=255)
                                                                                                                                 gATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAgg                 >  2:84670/1‑148 (MQ=255)
                                                                                                                                 gATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGc                <  5:7523/149‑1 (MQ=255)
                                                                                                                                       gaagaaCATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAAcaca          <  4:73386/149‑1 (MQ=255)
                                                                                                                                             cATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCaa    >  2:136733/1‑149 (MQ=255)
                                                                                                                                               tGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGTCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATg  <  1:55102/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                 
AATACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGCCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATG  >  NC_000913/2404713‑2405004

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CAATACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGCCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATGG  >  NC_000913/2404712‑2405005
                                                                                                                                                   |                                                                                                                                                  
CAATACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCAC                                                                                                                                                 <  NB501016:228:HFK2FAFXY:1:11204:13289:2446/151‑1 (MQ=60)
     CGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACC                                                                                                                                                >  NB501016:228:HFK2FAFXY:3:11611:14464:15097/1‑147 (MQ=60)
     CGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTC                                                                                                                                                   >  NB501016:228:HFK2FAFXY:2:11103:13342:12212/1‑144 (MQ=60)
      GCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGAT                                                                                                                                            >  NB501016:228:HFK2FAFXY:1:11310:9666:17233/1‑150 (MQ=60)
                          GCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGT                                                                                                                        <  NB501016:228:HFK2FAFXY:4:21506:22672:19289/150‑1 (MQ=60)
                                                        TCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCG                                                                                          <  NB501016:228:HFK2FAFXY:4:21409:20451:10357/150‑1 (MQ=60)
                                                                   TACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACA                                                                                                                             >  NB501016:228:HFK2FAFXY:1:11104:1624:10251/1‑104 (MQ=60)
                                                                                         GAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTG                                                        >  NB501016:228:HFK2FAFXY:1:21109:18433:11740/1‑151 (MQ=60)
                                                                                         GAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTG                                                        >  NB501016:228:HFK2FAFXY:3:11507:6944:10434/1‑151 (MQ=60)
                                                                                                  CATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGC                                               >  NB501016:228:HFK2FAFXY:1:21305:24321:12450/1‑151 (MQ=60)
                                                                                                              TACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAAC                                   >  NB501016:228:HFK2FAFXY:2:21201:5765:4849/1‑151 (MQ=60)
                                                                                                                                 AGATAACGAAGAACATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCA                <  NB501016:228:HFK2FAFXY:3:11405:1360:11751/151‑1 (MQ=60)
                                                                                                                                               ATGGTCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGTCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATGG  <  NB501016:228:HFK2FAFXY:1:11304:9637:7784/151‑1 (MQ=60)
                                                                                                                                                   |                                                                                                                                                  
CAATACGCACCAGATAAACCAGACCTGCCAGTAACACAAAAATAAAAATTGCAGCTTCCACAAAGCCTACCCAGCCGCTTTCGCGGATAGAGGTTGACCATGCGAACAGATACAGCGCTTCAACGTCGAAGATAACGAAGAACATGGCCACCAGATAAAACTTGGCGGACAGGCGTAAGCGGGCGGAGCCGACCGAGTCGATACCGGATTCAAACGGCACGTTTTTCGACCTCGCGCGTGCGCGACCGCCTAAAAACCAACCGCCTACCAGCATCAGGCAACACAGGCCAATGG  >  NC_000913/2404712‑2405005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑