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 434,130 C→T 39.9% intergenic (‑183/+106) fur ← / ← fldA DNA‑binding transcriptional dual regulator/flavodoxin 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE434,1300CT39.9% 40.7 / 56.8 85intergenic (‑183/+106)fur/fldADNA‑binding transcriptional dual regulator/flavodoxin 1
Reads supporting (aligned to +/- strand):  ref base C (32/19);  new base T (27/7);  total (59/26)
Fisher's exact test for biased strand distribution p-value = 1.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.28e-01

GTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCATTATCT  >  minE/434076‑434197
                                                      |                                                                   
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:2468372/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:2214577/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:282094/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:494295/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:3263533/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:2236482/68‑1 (MQ=255)
gTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACa                                                        <  1:3346722/68‑1 (MQ=255)
 ttAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAgg                                                      >  1:2740109/1‑69 (MQ=255)
     taaAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTac                                                   <  1:3124471/68‑1 (MQ=255)
       aaaaCGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTacaac                                                >  1:2184213/1‑69 (MQ=255)
       aaaaCGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTacaac                                                >  1:1842201/1‑69 (MQ=255)
       aaaaCGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTacaac                                                >  1:1291450/1‑69 (MQ=255)
       aaaaCGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTacaac                                                >  1:2045774/1‑69 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGGACACTGGGACATTGTACAGGTacaaca                                               >  1:452810/1‑67 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTacaaca                                               >  1:531479/1‑67 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTacaaca                                               >  1:2203909/1‑67 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTacaaca                                               >  1:157536/1‑67 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTacaaca                                               >  1:1638946/1‑67 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTacaac                                                >  1:3175354/1‑66 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2246972/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2217621/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2933749/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2631256/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2749722/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1036248/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:3368514/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:40389/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:479299/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:596565/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:652983/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:764707/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:845851/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1352322/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1026672/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:2029889/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1369616/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:106595/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1113306/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1389152/1‑68 (MQ=255)
          aCGTGGCACAGCTTACATTTACAACAGCAAGGCCACTTGAACACTGGGACATTGTACAGGTACAACAg                                              >  1:1162594/1‑68 (MQ=255)
              ggCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTg                                                            <  1:1328794/50‑1 (MQ=255)
                    gCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:908815/1‑69 (MQ=255)
                    gCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:827234/1‑69 (MQ=255)
                    gCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:242614/1‑69 (MQ=255)
                    gCTTACATTTACAACGGAAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:2151158/1‑69 (MQ=255)
                               cAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGc                         <  1:3043447/68‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:570183/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:1234045/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:378794/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:132372/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:1673028/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:596192/69‑1 (MQ=255)
                                        ggCCACTTGAACACTGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTg               <  1:2822994/69‑1 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:788724/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:83191/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:1343109/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:2137597/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:3051700/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:2131763/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:2101207/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:2404274/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:1833965/1‑69 (MQ=255)
                                         gCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGa              >  1:2532479/1‑69 (MQ=255)
                                           cACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGAtt            >  1:1349450/1‑69 (MQ=255)
                                           cACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGAtt            >  1:1147537/1‑69 (MQ=255)
                                             cTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTgg          <  1:3056949/69‑1 (MQ=255)
                                             cTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTgg          <  1:2487495/69‑1 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACCACAGCAAAAGTTACa                                   >  1:2881541/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:545367/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:2260065/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:1364255/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:1075247/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:2441031/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:3293677/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:505183/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:1233283/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:2707700/1‑42 (MQ=255)
                                               tGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACa                                   >  1:2711561/1‑42 (MQ=255)
                                                  acacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:1151402/67‑1 (MQ=255)
                                                  acacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:762421/67‑1 (MQ=255)
                                                  acacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:44214/67‑1 (MQ=255)
                                                  acacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:1791394/67‑1 (MQ=255)
                                                  acacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:1943389/67‑1 (MQ=255)
                                                   cacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:530159/66‑1 (MQ=255)
                                                   cacCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCAt       <  1:488832/66‑1 (MQ=255)
                                                     ccGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCATTATCt  >  1:3297197/1‑69 (MQ=255)
                                                     ccGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCATTATCt  >  1:2286478/1‑69 (MQ=255)
                                                      |                                                                   
GTTAATAAAAACGTGGCACAGCTTACATTTACAACGGCAAGGCCACTTGAACACCGGGACATTGTACAGGTACAACAGCAAAAGTTACAAATTTGTAGCAATTATTTTGATTGGCATTATCT  >  minE/434076‑434197

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