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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,012,700 C→T *105* (TAG→TAA)  fliE ← flagellar basal‑body component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,012,7000CT100.0% 173.6 / NA 55*105* (TAG→TAA) fliEflagellar basal‑body component
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/25);  total (30/25)

ACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACCTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCCACGCCGGGTTC  >  NC_000913/2012575‑2012828
                                                                                                                             |                                                                                                                                
aCGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGc                                                                                                                     <  1:689384/139‑1 (MQ=255)
  ggATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACATGCATGCtc                                                                                                                   >  1:141301/1‑139 (MQ=255)
   gATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCGCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtca                                                                                                                  <  2:309419/139‑1 (MQ=255)
      cGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtcatca                                                                                                               >  1:1086295/1‑139 (MQ=255)
       gTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtcatca                                                                                                               >  2:168456/1‑138 (MQ=255)
       gTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtcatca                                                                                                               <  1:168456/138‑1 (MQ=255)
                aGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATa                                                                                                     >  2:1321689/1‑139 (MQ=255)
                      cGTTCAGGATCAGGCATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATAcgccgc                                                                                               <  2:758462/139‑1 (MQ=255)
                        ttCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGcca                                                                                             <  2:1352897/139‑1 (MQ=255)
                          cAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGccacc                                                                                           <  1:1321689/139‑1 (MQ=255)
                                     aTCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACTTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACg                                                                                <  1:966596/139‑1 (MQ=255)
                                     aTCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACg                                                                                >  1:1323568/1‑139 (MQ=255)
                                     aTCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACg                                                                                >  1:585401/1‑139 (MQ=255)
                                       ccATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTa                                                                                                                                <  2:726723/89‑1 (MQ=255)
                                       ccATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTa                                                                                                                                >  1:726723/1‑89 (MQ=255)
                                                   aGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCa                                                                  <  1:752139/139‑1 (MQ=255)
                                                     aaaTTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCAtt                                                                <  2:585401/139‑1 (MQ=255)
                                                     aaaTTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCAtt                                                                >  1:453610/1‑139 (MQ=255)
                                                     aaaTTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCAtt                                                                >  1:957506/1‑139 (MQ=255)
                                                                  ttGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTg                                                   <  2:1323568/139‑1 (MQ=255)
                                                                   tGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGa                                                  <  2:453610/139‑1 (MQ=255)
                                                                      cccATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGc                                               <  2:957506/139‑1 (MQ=255)
                                                                         atccatGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCttt                                            >  2:1096581/1‑139 (MQ=255)
                                                                               gCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGc                                                                                                                         <  1:1171437/56‑1 (MQ=255)
                                                                               gCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGc                                                                                                                         >  2:1171437/1‑56 (MQ=255)
                                                                               gCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGccac                                                                                            >  2:353160/1‑85 (MQ=255)
                                                                               gCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGccac                                                                                            <  1:353160/85‑1 (MQ=255)
                                                                                    aCGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTg                                                   >  2:184996/1‑121 (MQ=255)
                                                                                    aCGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTg                                                   <  1:184996/121‑1 (MQ=255)
                                                                                     cgcgGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTa                                                                                                                                >  1:833574/1‑43 (MQ=255)
                                                                                     cgcgGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTa                                                                                                                                <  2:833574/43‑1 (MQ=255)
                                                                                     cgcgGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGt                                >  1:194086/1‑139 (MQ=255)
                                                                                     cgcgGTGAGATCGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCGGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGt                                >  2:1165125/1‑139 (MQ=255)
                                                                                                cGGATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGt                     >  1:73156/1‑139 (MQ=255)
                                                                                                  gATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCata                                     <  2:853113/121‑1 (MQ=255)
                                                                                                  gATGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCata                                     >  1:853113/1‑121 (MQ=255)
                                                                                                    tGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtcat                                                                                                                 <  1:351829/43‑1 (MQ=255)
                                                                                                    tGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCtcat                                                                                                                 >  2:351829/1‑43 (MQ=255)
                                                                                                    tGTAATTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTaa                 >  2:403724/1‑139 (MQ=255)
                                                                                                        aTTAACAACAGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAacgcc             >  2:1225859/1‑139 (MQ=255)
                                                                                                           aacaacAGGTTACAAAACTTACACCTGCATGCtcat                                                                                                                 >  1:14172/1‑36 (MQ=255)
                                                                                                           aacaacAGGTTACAAAACTTACACCTGCATGCtcat                                                                                                                 <  2:14172/36‑1 (MQ=255)
                                                                                                             caacaGGTTACAAAACTTACACCTGCATGCtcatca                                                                                                               <  1:318109/36‑1 (MQ=255)
                                                                                                             caacaGGTTACAAAACTTACACCTGCATGCtcatca                                                                                                               >  2:318109/1‑36 (MQ=255)
                                                                                                             caacaGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAacgccacgcc        >  1:791790/1‑139 (MQ=255)
                                                                                                              aacaGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCGGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCCACGCCg       <  1:1165125/139‑1 (MQ=255)
                                                                                                                caGGTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCCACGCCggg     >  2:724271/1‑139 (MQ=255)
                                                                                                                  ggTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATAcg                                                                                                   >  1:864854/1‑43 (MQ=255)
                                                                                                                  ggTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATAcg                                                                                                   <  2:864854/43‑1 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAg                                                 <  2:1298055/92‑1 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAg                                                 >  1:1298055/1‑92 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAacg               >  2:966088/1‑126 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCCACGCCGGGTTc  >  2:1012016/1‑139 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCAACGCCGAGTTc  >  1:1361907/1‑139 (MQ=255)
                                                                                                                   gTTACAAAACTTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCAAAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAacg               <  1:966088/126‑1 (MQ=255)
                                                                                                                             |                                                                                                                                
ACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAACAGGTTACAAAACCTACACCTGCATGCTCATCACTTCCTGATACGCCGCCACCAGCTTATTACGCACCTGAATCCCCATTTGCATAGAAACTGAGGCTTTTTGCATATCGGTCATCACATCGTTTAACGCCACGCCGGGTTC  >  NC_000913/2012575‑2012828

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