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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,040,713 C→T 22.9% D40D (GAC→GAT)  yqiH → predicted periplasmic pilin chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,040,7130CT22.9% 196.6 / 54.5 96D40D (GAC→GAT) yqiHpredicted periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base C (46/28);  new base T (10/12);  total (56/40)
Fisher's exact test for biased strand distribution p-value = 2.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.05e-01

CTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATAGAA  >  minE/2040644‑2040782
                                                                     |                                                                     
cTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACa                                                                      <  1:215809/71‑1 (MQ=255)
  gTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACa                                                                      >  1:3147952/1‑69 (MQ=255)
     tGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGc                                                                 >  1:3882292/1‑71 (MQ=255)
       agcagcATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCg                                                                <  1:395328/70‑1 (MQ=255)
       agcagcATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGa                                                               <  1:2421381/71‑1 (MQ=255)
        gcagcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCg                                                                >  1:2742142/1‑69 (MQ=255)
        gcagcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCg                                                                >  1:2163288/1‑69 (MQ=255)
         cagcaTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGaa                                                              <  1:537543/70‑1 (MQ=255)
            caTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCAt                                                          >  1:2133059/1‑71 (MQ=255)
             aTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCAtt                                                         <  1:3939197/71‑1 (MQ=255)
             aTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCAtt                                                         <  1:1450899/71‑1 (MQ=255)
             aTTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCAt                                                          >  1:3476852/1‑70 (MQ=255)
              ttGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCAtt                                                         >  1:706682/1‑70 (MQ=255)
              ttGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTa                                                        <  1:342467/71‑1 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                       >  1:2626648/1‑70 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                       >  1:1693825/1‑70 (MQ=255)
                gCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                       >  1:4013588/1‑70 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                      <  1:3488610/70‑1 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaaa                                                      <  1:2340398/70‑1 (MQ=255)
                 ccTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaaa                                                      <  1:289464/70‑1 (MQ=255)
                      ggTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTAc                                                >  1:1597760/1‑71 (MQ=255)
                         gCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGAc                                                                       >  1:2984575/1‑45 (MQ=255)
                         gCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGAc                                                                       >  1:1246020/1‑45 (MQ=255)
                          ccgtcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAAt                                            >  1:1781540/4‑71 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCAtt                                                         <  1:2290025/58‑1 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCAtt                                                         <  1:165729/58‑1 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAg                                                             <  1:197488/54‑1 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAg                                                             <  1:2531344/54‑1 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAg                                                             <  1:1456430/54‑1 (MQ=255)
                          ccATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAAt                                            >  1:443107/1‑71 (MQ=255)
                            atcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGa                                                               <  1:225130/50‑1 (MQ=255)
                            atcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaaa                                                      <  1:3578442/59‑1 (MQ=255)
                            atcatcCAGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATc                                           >  1:1577274/1‑70 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaa                                                       <  1:4138628/57‑1 (MQ=255)
                             tcatcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACt                                                   <  1:1529118/61‑1 (MQ=255)
                             tcataCCGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCa                                          >  1:3253758/1‑70 (MQ=255)
                               atcCCTGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                       >  1:1318620/1‑71 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAgg                                                                  >  1:2490831/1‑44 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCa                                                           >  1:2866402/1‑51 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCa                                          >  1:3108477/1‑68 (MQ=255)
                               atcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                       >  1:3412216/1‑71 (MQ=255)
                                tcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                       >  1:2944277/1‑70 (MQ=255)
                                tcCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                       >  1:1874150/1‑70 (MQ=255)
                                 cccGGATCGTACCCGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAg                                       >  1:1576177/1‑69 (MQ=255)
                                  ccGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTaaaa                                                     >  1:3975347/1‑54 (MQ=255)
                                  ccGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 >  1:2415945/1‑58 (MQ=255)
                                  ccGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 >  1:169045/1‑58 (MQ=255)
                                  ccGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTa                                     >  1:1182771/1‑70 (MQ=255)
                                   cGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                   <  1:3815019/71‑1 (MQ=255)
                                   cGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                   <  1:3332207/71‑1 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGACaaa                                                                    >  1:1642820/1‑37 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAAc                                                    >  1:1916109/1‑53 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                  <  1:3813970/71‑1 (MQ=255)
                                    ggATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                   >  1:1284225/1‑70 (MQ=255)
                                      aTCGTACCCGTATCATAATGAATGAGTAAGACAAAGGCGAAGCAtt                                                         <  1:3615155/46‑1 (MQ=255)
                                       tCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACt                                                   <  1:868927/51‑1 (MQ=255)
                                            cccGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGccc                          >  1:620191/1‑71 (MQ=255)
                                             ccGTATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCt                         <  1:592124/71‑1 (MQ=255)
                                             ccGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCt                         <  1:273616/71‑1 (MQ=255)
                                               gTATCATAATGAATGAGTCAGATAAAGGCGAAGCa                                                           >  1:3342288/1‑35 (MQ=255)
                                                tATCATAATGAATGAGTCAGATAAAGGCGAAGCATTaa                                                       >  1:2627695/1‑38 (MQ=255)
                                                tATCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATc                      <  1:497738/71‑1 (MQ=255)
                                                tATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 <  1:2439727/44‑1 (MQ=255)
                                                 aTCATAATGAATGAGTCAGACAAAGGCGAAGCAtt                                                         <  1:1589965/35‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                  <  1:78143/57‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                  <  1:3810541/57‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaaa                                 >  1:633222/1‑58 (MQ=255)
                                                  tCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCt                     <  1:403625/70‑1 (MQ=255)
                                                  tCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTg                    >  1:72166/1‑71 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACt                                                   >  1:4069185/1‑38 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 >  1:957768/1‑40 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 >  1:1465361/1‑40 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTa                                                 >  1:211229/1‑40 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCt                              >  1:2086476/1‑59 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTgg                   <  1:51381/70‑1 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGc                  >  1:872013/1‑71 (MQ=255)
                                                    aTAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGc                  >  1:3070476/1‑71 (MQ=255)
                                                     tAATGAATGAGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCaaa                                        <  1:217407/48‑1 (MQ=255)
                                                      aatgaatgAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTAta                      >  1:1664009/1‑64 (MQ=255)
                                                      aatgaatgAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGcc                 >  1:117439/1‑70 (MQ=255)
                                                       atgaatgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                   >  1:3075505/1‑51 (MQ=255)
                                                        tgaatgaGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaaa                                 >  1:1709966/1‑52 (MQ=255)
                                                           atgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTTCCCTATCTGGCCCaaa             <  1:1993361/69‑1 (MQ=255)
                                                           atgaGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACa           >  1:1830585/1‑71 (MQ=255)
                                                              aGTCAGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACa           >  1:588728/1‑68 (MQ=255)
                                                              aGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaaa                                  <  1:765742/45‑1 (MQ=255)
                                                              aGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATg         <  1:417691/70‑1 (MQ=255)
                                                                tCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATgg        <  1:2825369/69‑1 (MQ=255)
                                                                  aGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTaaa                                   <  1:3247396/40‑1 (MQ=255)
                                                                  aGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGa       >  1:2728269/1‑68 (MQ=255)
                                                                  aGATAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGa       >  1:3213894/1‑68 (MQ=255)
                                                                  aGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGa       >  1:3318513/1‑68 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGGTagaa  <  1:2660476/71‑1 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATag    >  1:553789/1‑69 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATag    >  1:2232416/1‑69 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATag    >  1:3914240/1‑69 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATag    >  1:1355005/1‑69 (MQ=255)
                                                                    aCAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATag    >  1:882165/1‑69 (MQ=255)
                                                                     cAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAAc            >  1:2729769/1‑60 (MQ=255)
                                                                     cAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATagaa  <  1:1130940/70‑1 (MQ=255)
                                                                     |                                                                     
CTGTATGAGCAGCATTGCCTGGGGTGCCATCATCCCGGATCGTACCCGTATCATAATGAATGAGTCAGACAAAGGCGAAGCATTAAAACTTACTAATCAAAGTAAAAACCTGCCCTATCTGGCCCAAACATGGATAGAA  >  minE/2040644‑2040782

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