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 2,198,231 C→T 32.9% R250R (CGC→CGT)  degS → serine endoprotease, periplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,198,2310CT32.9% 83.0 / 49.7 97R250R (CGC→CGT) degSserine endoprotease, periplasmic
Reads supporting (aligned to +/- strand):  ref base C (53/12);  new base T (22/10);  total (75/22)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.97e-01

Only 100 of 108 total aligned reads displayed.

ACGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTG  >  minE/2198163‑2198288
                                                                    |                                                         
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:2357527/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:312196/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:1442054/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           >  1:1677819/1‑69 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:1305624/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:1919632/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:3423558/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:2528059/69‑1 (MQ=255)
aCGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:2314086/69‑1 (MQ=255)
      gAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:1048416/63‑1 (MQ=255)
         ggTATCTGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCcgc                                                           <  1:2739785/60‑1 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:2095039/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:2685100/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:798341/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:2026923/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:2346750/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:393474/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:3165716/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:1348301/1‑68 (MQ=255)
          gTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTcgc                                                  >  1:3167188/1‑68 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGt                                                >  1:3426427/1‑68 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGt                                                >  1:1556228/1‑68 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               >  1:1725709/1‑69 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               <  1:2103773/69‑1 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               >  1:452110/1‑69 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               <  1:1930188/69‑1 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               <  1:3213058/69‑1 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               <  1:240445/69‑1 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               <  1:1669862/69‑1 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               >  1:863455/1‑69 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTg                                               >  1:2811613/1‑69 (MQ=255)
            aTCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCAGCGATGGTCGCGTg                                               >  1:1074454/1‑69 (MQ=255)
                        aTTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTa                                    <  1:26263/68‑1 (MQ=255)
                         ttCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTa                                    <  1:77644/67‑1 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATg                                                       >  1:1104150/1‑37 (MQ=25)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:1012405/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:37240/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:2425672/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:2494395/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:3061288/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:422234/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:438323/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:757694/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:2709895/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:752967/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:2737701/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:549232/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:1348589/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:1275114/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:87457/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:1493182/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:11703/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:113637/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAACTGATCCGTGATGGCCGTGTGATCCGTGGCTAcattggcattgg                        >  1:2082366/1‑68 (MQ=255)
                                    ttAGCGACCAAAATTATGGATAAAATGATCCGTGATGGCcg                                                   >  1:1038183/1‑41 (MQ=19)
                                     tAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcg                      >  1:2184773/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcgg                     >  1:2671102/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcgg                     >  1:1800168/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcgg                     >  1:1645328/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcgg                     >  1:2507529/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcgg                     >  1:3009184/1‑69 (MQ=255)
                                      aGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcggcg                      >  1:2428023/1‑68 (MQ=255)
                                         aaCCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGAc                   >  1:3083623/1‑68 (MQ=255)
                                            cAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGAc                   >  1:2768212/1‑65 (MQ=255)
                                            cAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGAc                   >  1:736118/1‑65 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATcg                         >  1:1329095/1‑55 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:1126991/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:3237292/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:91353/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:2285079/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:466885/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:1432305/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:1581708/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:204287/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:2551247/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTgag              >  1:783800/1‑66 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTga               >  1:894326/1‑65 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTga               >  1:1473696/1‑65 (MQ=255)
                                                aTTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTga               >  1:103645/1‑65 (MQ=255)
                                                aTTATGGATAAGCTGATACGCGAAGGTCGCGTGATCCGCGGCTACATTgg                              >  1:21370/1‑50 (MQ=255)
                                                     ggATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcac       <  1:819860/68‑1 (MQ=255)
                                                     ggATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcac       <  1:962678/68‑1 (MQ=255)
                                                     ggATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcac       <  1:1102579/68‑1 (MQ=255)
                                                     ggATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcac       <  1:3127900/68‑1 (MQ=255)
                                                     ggATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcac       <  1:2349419/68‑1 (MQ=255)
                                                      gATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcacca     >  1:3340877/1‑69 (MQ=255)
                                                      gATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGcacca     >  1:202966/1‑69 (MQ=255)
                                                         aaGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTg  >  1:3336146/1‑69 (MQ=255)
                                                         aaGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTg  >  1:1432970/1‑69 (MQ=255)
                                                         aaGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTg  >  1:1481799/1‑69 (MQ=255)
                                                         aaGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTg  >  1:2706315/1‑69 (MQ=255)
                                                         aaGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTg  >  1:2819922/1‑69 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:2715422/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:2325445/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:1934950/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:1532048/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:641597/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:3045935/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:3213427/57‑1 (MQ=255)
                                                             tGATCCGTGATGGCCGTGTGATCCGTGGCTACATTGGCATTGGTGGACGTGAGATCg          <  1:1032583/57‑1 (MQ=255)
                                                                    |                                                         
ACGCCGGAAGGTATCGGCTTTGCGATTCCTTTCCAGTTAGCAACCAAAATTATGGATAAGCTGATCCGCGATGGTCGCGTGATCCGCGGCTACATTGGTATCGGCGGACGTGAGATCGCACCACTG  >  minE/2198163‑2198288

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