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 1,628,383 C→T 64.6% L221L (TTG→TTA)  ypfG ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,628,3830CT64.6% 59.3 / 55.6 93L221L (TTG→TTA) ypfGhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/8);  new base T (28/32);  total (53/40)
Fisher's exact test for biased strand distribution p-value = 8.61e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCGT  >  minE/1628318‑1628444
                                                                 |                                                             
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGTCGTaac                                                            <  1:439441/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2142014/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2951576/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2985051/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:1696109/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:3165091/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:1272623/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2219849/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:180652/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:1821327/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2812422/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:3401381/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:1023946/69‑2 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:1784294/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:3436061/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:2110673/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:1452777/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:620996/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:1541704/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:694105/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:951361/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:1134219/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:1027701/1‑68 (MQ=255)
gCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCaa                                                             >  1:383762/1‑68 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:395860/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:258446/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:966513/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:1030199/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:399788/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:975939/67‑1 (MQ=255)
   tCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATg                                                           <  1:3158880/67‑1 (MQ=255)
                 catcaGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGc                                                               <  1:2184338/49‑1 (MQ=255)
                 catcaGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGc                                                               <  1:3356374/49‑1 (MQ=255)
                    caGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAg                                        >  1:985373/1‑69 (MQ=255)
                    caGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAg                                        >  1:2270898/1‑69 (MQ=255)
                    caGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAg                                        >  1:956431/1‑69 (MQ=255)
                      gcgcTTTATCATCGGTCAGCGCAGTGACATTCACCTCACGACGTaac                                                            <  1:2560929/47‑2 (MQ=37)
                                       agCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGag                                                <  1:3088599/42‑1 (MQ=255)
                                        gcgcAGTGACATTCACATCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTc                    >  1:391050/1‑69 (MQ=255)
                                               gACATTCACCTCATGACGCAATGGATCAAGCGAGCAGCGCAGACCa                                    >  1:2944150/1‑46 (MQ=255)
                                                aCATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATc             >  1:2888668/1‑68 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:2771362/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:3343613/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:351279/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:3137395/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:377655/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:1023689/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:2215407/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:2096289/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:1948788/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:819451/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:425384/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:486458/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:1681432/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:782431/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:1442692/65‑1 (MQ=255)
                                                  aTTCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:1362702/65‑1 (MQ=255)
                                                   ttCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:2162789/64‑1 (MQ=255)
                                                    tCACCTCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              <  1:2414318/63‑1 (MQ=255)
                                                     cACCTCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCaa       >  1:393782/1‑69 (MQ=255)
                                                     cACCTCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCaa       >  1:2244380/1‑69 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:604797/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:81655/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:3377761/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2527519/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1944028/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1015971/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1069727/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1164926/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1248681/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1301207/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1358577/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1517481/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:154363/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1636845/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1727356/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2061405/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2179851/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2667735/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:3096793/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:3068855/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:304776/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2858975/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2808435/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2807311/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:226834/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:1010909/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGCCAGTTTCCATAAt              >  1:2312823/1‑58 (MQ=255)
                                                         tCACGACGTAACGGATCAAGCGAACAGCGCAGACCATTCATCCGACAGTTTCCATAAt              >  1:1171009/1‑58 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCg   >  1:248232/1‑68 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCg   >  1:2344313/1‑68 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCg   >  1:190348/1‑68 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCGt  >  1:589045/1‑69 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCGt  >  1:3149325/1‑69 (MQ=255)
                                                          cACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCGt  >  1:1023876/1‑69 (MQ=255)
                                                                 |                                                             
GCCTCACAGCTAATCATCATCAGCGCTTTATCATCAGTCAGCGCAGTGACATTCACCTCACGACGCAATGGATCAAGCGAGCAGCGCAGACCATTCATCCGCCAGTTTCCATAATCCAGCAAATCGT  >  minE/1628318‑1628444

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