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 2,720,384 C→T 57.2% T399T (ACG→ACA)  yhfK ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,720,3840CT57.2% 23.9 / 70.5 91T399T (ACG→ACA) yhfKconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (32/7);  new base T (27/25);  total (59/32)
Fisher's exact test for biased strand distribution p-value = 3.78e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAC  >  minE/2720323‑2720450
                                                             |                                                                  
cGGAGCGATTTACAATCCTCAGCCGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:106501/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:1850022/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:523006/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:2461711/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:1600094/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:598974/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:1509006/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:297383/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:2971193/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:2562830/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc                                                              >  1:2098735/1‑68 (MQ=255)
cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtaatc                                                              >  1:886134/1‑68 (MQ=255)
  gAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAgg                                                           <  1:3316272/69‑1 (MQ=255)
   aGCGATTCACACTCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa                                                          <  1:912907/69‑1 (MQ=255)
   aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa                                                          <  1:1371769/69‑1 (MQ=255)
   aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa                                                          <  1:862371/69‑1 (MQ=255)
   aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa                                                          <  1:2816951/69‑1 (MQ=255)
          cacaATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGt                                                    >  1:2047236/1‑68 (MQ=255)
          cacaATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGt                                                    >  1:3316049/1‑68 (MQ=255)
                ccTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACtt                                             >  1:167969/1‑69 (MQ=255)
                ccTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACtt                                             >  1:3406609/1‑69 (MQ=255)
                ccTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACtt                                             >  1:2604638/1‑69 (MQ=255)
                ccTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACt                                              >  1:2055306/1‑68 (MQ=255)
                       cGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGa                                      >  1:615292/1‑69 (MQ=255)
                                     gCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGc                                         >  1:531581/1‑52 (MQ=255)
                                     gCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCa                                        >  1:1546551/1‑53 (MQ=255)
                                     gCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCa                                        >  1:1401104/1‑53 (MQ=255)
                                     gCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCa                                        >  1:1678155/1‑53 (MQ=255)
                                        aTTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGcac                       <  1:2961557/67‑3 (MQ=255)
                                        aTTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCAt                     <  1:2537246/69‑1 (MQ=255)
                                           ttGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAg                  >  1:2666117/1‑69 (MQ=255)
                                           ttGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAg                  >  1:163139/1‑69 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:2362532/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:1266342/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:101813/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:1300432/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:2999726/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:1861462/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:34572/1‑68 (MQ=255)
                                                tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg              >  1:165541/1‑68 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAgc                                >  1:1083234/1‑48 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGc            >  1:2072536/1‑68 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:2305690/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:2415206/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:2629825/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:205312/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:2038795/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa           >  1:1225798/1‑69 (MQ=255)
                                                  aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCAACAGGCTGGCa           >  1:2664843/1‑69 (MQ=255)
                                                     aGCAATTCTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:439285/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGTCAACg        >  1:2818111/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAAc         >  1:2074186/1‑68 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:3040342/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:91146/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:976443/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:2260946/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:2082796/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:1841180/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:1700233/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:1580990/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:1560639/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:2129973/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATCCAGTAAGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:791387/1‑69 (MQ=255)
                                                     aGCAATACTGTCATCAGGATACAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg        >  1:1920057/1‑69 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1415707/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1425729/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:811347/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:810226/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1800525/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1216817/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:510614/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:109856/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1786750/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1058988/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:3025712/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2171239/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2128356/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2853626/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:285506/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2097184/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2092407/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:2481854/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1894956/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:3180789/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:3237501/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1846014/69‑1 (MQ=255)
                                                        aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCACATCAGGCTGGCAACGCtt     <  1:3297503/69‑1 (MQ=255)
                                                         aTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:1698358/68‑1 (MQ=255)
                                                         aTACTGTCATCAGGATCCAGTACGACTTCAGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt     <  1:411023/68‑1 (MQ=255)
                                                           aCCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc  >  1:1528162/1‑69 (MQ=255)
                                                           aCCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc  >  1:27504/1‑69 (MQ=255)
                                                            ccGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc  >  1:914115/1‑68 (MQ=255)
                                                             |                                                                  
CGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAC  >  minE/2720323‑2720450

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