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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,040,713 C→T 71.3% D40D (GAC→GAT)  yqiH → predicted periplasmic pilin chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,040,7130CT71.3% 137.2 / 70.8 101D40D (GAC→GAT) yqiHpredicted periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base C (16/13);  new base T (40/32);  total (56/45)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

Only 100 of 104 total aligned reads displayed.

CTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATAGA  >  minE/2040644‑2040781
                                                                     |                                                                    
cTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGAc                                                                      >  1:2993875/1‑70 (MQ=255)
cTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGAc                                                                      <  1:419919/70‑1 (MQ=255)
    aTGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAgg                                                                 >  1:437376/1‑71 (MQ=255)
    aTGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAgg                                                                 >  1:63719/1‑71 (MQ=255)
     tGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAgg                                                                 <  1:3896839/70‑1 (MQ=255)
        gcagcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCg                                                               >  1:4229056/1‑69 (MQ=255)
         cagcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAg                                                            >  1:5531291/1‑71 (MQ=255)
           gcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCa                                                          >  1:3483939/1‑71 (MQ=255)
           gcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCa                                                          <  1:5197208/71‑1 (MQ=255)
               tGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTa                                                       >  1:4586187/1‑70 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaa                                                      >  1:3420838/1‑70 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                      <  1:1436613/70‑1 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                      >  1:2861132/1‑70 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                      <  1:651076/70‑1 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                     <  1:4335640/70‑1 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                     <  1:792642/70‑1 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                     <  1:1885035/70‑1 (MQ=255)
                   tGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACt                                                  >  1:2968218/1‑71 (MQ=255)
                     gggTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACt                                                  <  1:3641484/69‑1 (MQ=255)
                         gCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTaa                                            >  1:383823/1‑71 (MQ=255)
                         gCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTaa                                            >  1:1231425/1‑71 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACaa                                                                    >  1:3891850/1‑46 (MQ=255)
                            atcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCa                                         <  1:5373964/71‑1 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATaa                                                                    <  1:1826918/43‑1 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAg                                                            <  1:1810569/51‑1 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAg                                                            <  1:229479/51‑1 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCa                                         >  1:2754533/1‑70 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCa                                         >  1:3151521/1‑70 (MQ=255)
                              catcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:2181694/1‑62 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGc                                                           <  1:3579068/50‑1 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGc                                                           <  1:1143437/50‑1 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                      >  1:2640228/1‑71 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                      >  1:5170603/1‑71 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                      >  1:5528527/1‑71 (MQ=255)
                               atcCCGGATCGTACCCGTATCAAAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                      >  1:2191793/1‑71 (MQ=255)
                                tcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACt                                                  >  1:707717/1‑58 (MQ=255)
                                tcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGt                                     <  1:4777192/71‑1 (MQ=255)
                                tcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTaa                                            <  1:821514/64‑1 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaaa                                                    >  1:4104647/1‑55 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaaa                                                    >  1:181324/1‑55 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaaa                                                    >  1:4871220/1‑55 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACtt                                                 <  1:3662611/58‑1 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGt                                     >  1:4182031/1‑70 (MQ=255)
                                  ccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCa                                         <  1:2915699/65‑1 (MQ=255)
                                   cGGATCGTACCCGTATCATAATGAATGAGTCAGAc                                                                      <  1:625450/35‑1 (MQ=255)
                                   cGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                  <  1:3472980/71‑1 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 <  1:1577379/71‑1 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 <  1:3891554/71‑1 (MQ=255)
                                     gATCGTACACGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaaa                                <  1:5601418/71‑1 (MQ=255)
                                      aTCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaa                                   >  1:3977572/1‑67 (MQ=255)
                                      aTCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAAc                               <  1:5191645/71‑1 (MQ=255)
                                        cGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACt                                              >  1:4419975/1‑54 (MQ=255)
                                        cGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACt                                              >  1:2816021/1‑54 (MQ=255)
                                        cGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 >  1:790069/1‑67 (MQ=255)
                                        cGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 >  1:5594576/1‑67 (MQ=255)
                                         gTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCt                             <  1:3030952/70‑1 (MQ=255)
                                          tACCCTTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                  <  1:3189162/64‑1 (MQ=255)
                                          tACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAg                                                            <  1:1709363/38‑1 (MQ=255)
                                            cccGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGccc                         >  1:962432/1‑71 (MQ=255)
                                             ccGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCt                        <  1:1895207/71‑1 (MQ=255)
                                             ccGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCt                        <  1:1606915/71‑1 (MQ=255)
                                               gTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTAt                      >  1:1517989/1‑71 (MQ=255)
                                                 aTCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                      <  1:5607749/53‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                     <  1:4428931/37‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 >  1:2514242/1‑57 (MQ=255)
                                                  tCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 >  1:4290152/1‑57 (MQ=255)
                                                  tCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCt                    <  1:1328881/70‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGACAAACGCGAAGCATTaa                                                      <  1:1354498/36‑1 (MQ=255)
                                                  tCATAATGAATGAATCAGATAAAGGCGAAGCATTaaa                                                     <  1:1984899/37‑1 (MQ=38)
                                                   cATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTgg                  >  1:5407799/1‑71 (MQ=255)
                                                   cATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTgg                  >  1:5358253/1‑71 (MQ=255)
                                                   cATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCt                    <  1:4701448/69‑1 (MQ=255)
                                                    aTAATGAATGAGTCAGATAAAGGCGAAGCATTAAAAc                                                   >  1:708791/1‑37 (MQ=255)
                                                    aTAATGAATGAGTCAGATAAAGGCGAAGCATTAAAAc                                                   >  1:3880911/1‑37 (MQ=255)
                                                    aTAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATc                     >  1:3648247/1‑67 (MQ=255)
                                                    aTAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGc                 >  1:2885734/1‑71 (MQ=255)
                                                     tAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGcc                <  1:840087/71‑1 (MQ=255)
                                                     tAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGcc                <  1:2855168/71‑1 (MQ=255)
                                                     tAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTAc                                               <  1:979333/40‑1 (MQ=255)
                                                     tAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTAc                                               <  1:4199807/40‑1 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACtt                                                 >  1:5226847/1‑37 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:1849502/1‑38 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:1409175/1‑38 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:2350524/1‑38 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:1620490/1‑38 (MQ=255)
                                                      aatgaatgAGTCAGATAAAGGCGAAGCATTAAAACTTa                                                >  1:4351073/1‑38 (MQ=255)
                                                       atgaatgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGccc               <  1:1287071/70‑1 (MQ=255)
                                                       atgaatgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCa              <  1:231056/71‑1 (MQ=255)
                                                        tgaatgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCa              >  1:1966648/1‑70 (MQ=255)
                                                        tgaatgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCa              >  1:5076649/1‑70 (MQ=255)
                                                         gaatgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATc                                          >  1:2840409/1‑41 (MQ=255)
                                                         gaatgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAAc                               >  1:1342980/1‑52 (MQ=255)
                                                         gaatgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                 >  1:1082257/1‑50 (MQ=255)
                                                           atgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaaa                                >  1:2042800/1‑49 (MQ=255)
                                                           atgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACa          <  1:1356822/71‑1 (MQ=255)
                                                           atgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACa          <  1:3791898/71‑1 (MQ=255)
                                                            tgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTAt                      >  1:4544348/1‑58 (MQ=255)
                                                             gaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATg        >  1:1911728/1‑71 (MQ=255)
                                                                 cAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTTCCCTATCTGGCCCAAACATGGa      >  1:5646023/1‑69 (MQ=255)
                                                                   gACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATaga  <  1:5530946/71‑1 (MQ=255)
                                                                     |                                                                    
CTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATAGA  >  minE/2040644‑2040781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A