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
A14 F1 I1 R1 770 68.5 3470224 91.7% 3182195 103.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,432,994 (C)6→7 coding (567/1125 nt) smf ← DNA recombination‑mediator A family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,432,9881.C100.0% 173.0 / NA 49G191G (GGC→GGG) smfDNA recombination‑mediator A family protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (26/23);  total (26/23)

CACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCGATT  >  NC_000913/3432856‑3433120
                                                                                                                                     |                                                                                                                                     
cACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑cccccc                                                                                                                                <  1:384084/139‑1 (MQ=255)
 aCCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑ccccccc                                                                                                                               <  2:471992/139‑2 (MQ=255)
         aCCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑ccccc                                                                                                                                 >  2:1266122/1‑129 (MQ=255)
         aCCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑ccccc                                                                                                                                 <  1:1266122/129‑1 (MQ=255)
                   aaaGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATCATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCa                                                                                                              >  2:1228918/1‑139 (MQ=255)
                     aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGa                                                                                                                    >  1:353222/1‑131 (MQ=255)
                     aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGa                                                                                                                    <  2:353222/131‑1 (MQ=255)
                     aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGc                                                                                                            >  1:1291735/1‑139 (MQ=255)
                                ccaccaGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCAt                                                                                                 <  1:1228918/139‑1 (MQ=255)
                                   ccaGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAc                                                                                              >  1:777429/1‑139 (MQ=255)
                                     aGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg                                                                                            <  2:777429/139‑1 (MQ=255)
                                       tACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggc                                                                                           >  2:94544/1‑139 (MQ=255)
                                          acCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCgggg                                                                                       <  1:1431850/139‑1 (MQ=255)
                                                aCTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt                                                                                 <  2:1291735/139‑1 (MQ=255)
                                                 cTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAgcg‑‑c                                                                                                                                     <  1:1605476/85‑1 (MQ=255)
                                                 cTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAgcg‑‑c                                                                                                                                     >  2:1605476/1‑85 (MQ=255)
                                                      aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTAtt                                                                           >  1:873723/1‑139 (MQ=255)
                                                           tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCgggg                                                                                       <  2:258979/122‑1 (MQ=255)
                                                           tGATAATGCGATTTCGTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGCCAGCCAGTCGGGCATGACGGCgggg                                                                                       >  1:258979/1‑122 (MQ=255)
                                                                aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTc                                                                 >  1:244738/1‑139 (MQ=255)
                                                                aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑ccccccctgt                                                                                                                            >  2:417461/1‑75 (MQ=255)
                                                                aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑ccccccctgt                                                                                                                            <  1:417461/79‑5 (MQ=255)
                                                                     aTTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGTATGGTATTAAGTCCATTccc                                                               >  1:1549465/1‑136 (MQ=255)
                                                                     aTTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGTATGGTATTAAGTCCATTccc                                                               <  2:1549465/136‑1 (MQ=255)
                                                                       ttcttcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCa                                                                                                                      >  1:329411/1‑79 (MQ=255)
                                                                       ttcttcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCa                                                                                                                      <  2:329411/79‑1 (MQ=255)
                                                                         cttcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggcg                                                                                          <  1:1656461/105‑1 (MQ=255)
                                                                         cttcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggcg                                                                                          >  2:1656461/1‑105 (MQ=255)
                                                                                        tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATa                                                          >  1:664874/1‑122 (MQ=255)
                                                                                        tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATa                                                          <  2:664874/122‑1 (MQ=255)
                                                                                           gCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                                      <  2:244738/139‑1 (MQ=255)
                                                                                           gCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                                      <  2:1406670/139‑1 (MQ=255)
                                                                                              aGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCa                                                     >  2:1254979/1‑121 (MQ=255)
                                                                                              aGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCa                                                     <  1:1254979/121‑1 (MQ=255)
                                                                                               ggggTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg                                                                                            <  2:1651795/81‑1 (MQ=255)
                                                                                               ggggTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg                                                                                            >  1:1651795/1‑81 (MQ=255)
                                                                                                     gAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCa                                         <  2:975690/126‑1 (MQ=255)
                                                                                                     gAACATCGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCa                                         >  1:975690/1‑126 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTg                                                                                                                 <  1:1008808/48‑1 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTg                                                                                                                 >  2:1008808/1‑48 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                                        >  1:63369/1‑57 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                                        >  2:336631/1‑57 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                                        <  1:336631/57‑1 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                                        <  2:63369/57‑1 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa                               <  2:247835/130‑1 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa                               >  1:247835/1‑130 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCtt                      >  2:298825/1‑139 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCtt                      >  2:476946/1‑139 (MQ=255)
                                                                                                           cGAGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCtt                      >  2:93056/1‑139 (MQ=255)
                                                                                                             aGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACa                                                        <  1:886802/103‑1 (MQ=255)
                                                                                                             aGGGGAAATTCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACa                                                        >  2:886802/1‑103 (MQ=255)
                                                                                                                     ttCCGAGACGAGAGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTac            <  2:873723/139‑1 (MQ=255)
                                                                                                                            acgagaGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTaa                                                                         <  1:1487036/71‑1 (MQ=255)
                                                                                                                            acgagaGCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTaa                                                                         >  2:1487036/1‑71 (MQ=255)
                                                                                                                               agagCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                                  <  2:215152/59‑1 (MQ=255)
                                                                                                                               agagCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                                  >  1:215152/1‑59 (MQ=255)
                                                                                                                               agagCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCGAtt  >  2:791326/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                                     
CACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCGATT  >  NC_000913/3432856‑3433120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A