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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,693,488 G→A 55.6% T380T (ACC→ACT)  yrfF ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,693,4880GA55.6% 10.3 / 49.5 63T380T (ACC→ACT) yrfFpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (15/13);  new base A (9/26);  total (24/39)
Fisher's exact test for biased strand distribution p-value = 3.65e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGA  >  minE/2693423‑2693555
                                                                 |                                                                   
cccTTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTCTTTTACGCtggt                                                                   >  1:2376564/1‑68 (MQ=255)
cccGTAGCGCTAATACGCAATGTATCGCCTACCCGCACGCGAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:437033/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:2935304/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:691575/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:2488003/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:2525651/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:2571630/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:2621191/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:872132/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:424196/1‑69 (MQ=255)
cccGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCtggtg                                                                  >  1:1231354/1‑69 (MQ=255)
      ccGCTGATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:1938332/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTc                                                             >  1:3018324/1‑68 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:63215/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:3146255/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:2338823/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:1309084/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:1574177/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:464452/1‑69 (MQ=255)
      ccGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCa                                                            >  1:3090432/1‑69 (MQ=255)
         cTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATg                                                         <  1:3304354/69‑1 (MQ=255)
         cTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATg                                                         <  1:2255877/69‑1 (MQ=255)
               cGCAATGTATCGCCTACCCGTACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGc                                                                <  1:709320/56‑1 (MQ=255)
               cGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGc                                                                <  1:463164/56‑1 (MQ=255)
               cGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGc                                                                <  1:2317823/56‑1 (MQ=255)
               cGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGc                                                                <  1:602386/56‑1 (MQ=255)
                   aTGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTgcgcgc                                               <  1:2783080/69‑1 (MQ=255)
                      tATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGcc                                              >  1:547029/1‑67 (MQ=255)
                      tATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCt                                             >  1:3043690/1‑68 (MQ=255)
                          gCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTc                                          >  1:2631614/1‑67 (MQ=255)
                          gCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCa                                         >  1:821254/1‑68 (MQ=255)
                          gCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCa                                         >  1:3085705/1‑68 (MQ=255)
                          gCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCa                                         >  1:1830708/1‑68 (MQ=255)
                            cTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATc                                       <  1:3299869/68‑1 (MQ=255)
                            cTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATc                                       <  1:1333634/68‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1020046/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1118202/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1540835/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:289650/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:2660046/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1768050/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1821877/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:2570630/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:2149497/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1822066/69‑1 (MQ=255)
                                       ccAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1894175/69‑1 (MQ=255)
                                        cAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTgcgcgc                                               <  1:506164/48‑1 (MQ=255)
                                        cAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:1596151/68‑1 (MQ=255)
                                        cAGCGTCAGCCAGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:801733/68‑1 (MQ=255)
                                                   aGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGc               <  1:237739/69‑1 (MQ=255)
                                                   aGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGc               <  1:1748982/69‑1 (MQ=255)
                                                   aGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGc               <  1:1905671/69‑1 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:639932/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:1266387/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2011054/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2261112/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2293817/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:583849/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2958605/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2559949/1‑68 (MQ=255)
                                                   aGTTGTTTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCgg                >  1:2613838/1‑68 (MQ=255)
                                                      tgttTTACGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:491914/54‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGTCATATCCAg       <  1:1030195/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:3203414/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:2928127/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:503651/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:759068/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:2523567/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:2376421/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:693119/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:1993955/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:633029/68‑1 (MQ=255)
                                                            aCGCTAGTGGCTTCAATGGTCTGCGCGCCTTTCACCCACGAGAGGGTGAATTTCAGCGGCATATCCAg       <  1:3076489/68‑1 (MQ=255)
                                                              gCTAGTGGCTTCAATGGTCTGCGCGCCTTTCATCCACGAGAGGGTg                           <  1:2021269/46‑1 (MQ=38)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:2061196/69‑1 (MQ=255)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:2145360/69‑1 (MQ=255)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:2633907/69‑1 (MQ=255)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:1491182/69‑1 (MQ=255)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:1040745/69‑1 (MQ=255)
                                                                tggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:992224/69‑1 (MQ=255)
                                                                tggtgaCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:1305160/69‑1 (MQ=255)
                                                                 ggtggCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGa  <  1:1910115/68‑1 (MQ=255)
                                                                 |                                                                   
CCCGTACCGCTAATACGCAATGTATCGCCTACCCGCACGCCAGCGTCAGCCAGTTGTTTTACGCTGGTGGCTTCAATGGTCTGCGCGCCTTTCATCCATGAGAGAGTGAATTTCAGCGGCATATCCAGCGGGA  >  minE/2693423‑2693555

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