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 1,283,662 A→C 31.5% E1814A (GAG→GCG)  yeeJ → adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,283,6620AC31.5% 127.4 / 107.1 143E1814A (GAG→GCG) yeeJadhesin
Reads supporting (aligned to +/- strand):  ref base A (43/55);  new base C (13/32);  total (56/87)
Fisher's exact test for biased strand distribution p-value = 9.96e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.95e-01

Only 100 of 149 total aligned reads displayed.

TAAAGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAGGT  >  minE/1283597‑1283728
                                                                 |                                                                  
tAAAGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGcc                                                                 >  1:3082618/1‑69 (MQ=255)
tAAAGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGcc                                                                 >  1:2844534/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGcc                                                                 >  1:2420070/1‑68 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:84766/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:2454369/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:235274/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:1260548/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:2653545/1‑69 (MQ=255)
 aaaGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCa                                                                >  1:483828/1‑69 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTTCAGAGCCATCCTCGCa                                                        <  1:2538338/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1626946/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2497275/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2987925/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2921562/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1850185/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2030673/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2664338/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:2503297/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:3376885/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1355326/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1281087/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1440732/68‑1 (MQ=255)
          gTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1399501/68‑1 (MQ=255)
                gACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGatc                                                 <  1:286860/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:2234343/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:2785650/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:2797582/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:651460/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:197313/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:611915/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:1254919/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:1784725/69‑1 (MQ=255)
                    aGTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:1230958/69‑1 (MQ=255)
                     gTTTGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:1991760/68‑1 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:677780/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:2651329/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:705968/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:3392176/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:1284713/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:2774322/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:1728508/1‑66 (MQ=255)
                       ttGGCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             >  1:440205/1‑66 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATg                                                    >  1:2551830/1‑58 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGcc                                          >  1:2748938/1‑68 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGcc                                          >  1:570494/1‑68 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGcc                                          >  1:3131248/1‑68 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGcc                                          >  1:900647/1‑68 (MQ=255)
                        tGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGcc                                          >  1:1927183/1‑68 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTTACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:310945/68‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCa                                                        <  1:1230116/52‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:893808/68‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:315804/68‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:3088320/68‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:166625/68‑1 (MQ=255)
                          gCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:1838950/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:1101434/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:2460026/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:700518/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:58520/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:333106/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:3087929/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:3086385/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:1767154/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:2053625/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:2770623/68‑1 (MQ=255)
                          gCAACCCGGTGACGCATCAACCCGCGACATTCAGTGCAGCGCCATCCTCGCAAATGATCATCAGCCAg                                        <  1:2273663/68‑1 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:390221/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:841837/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:1166542/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:2563652/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:14359/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:1505943/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:1956498/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:2149924/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:2717074/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:2113080/1‑69 (MQ=255)
                                cGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACgg                                 >  1:1631440/1‑69 (MQ=255)
                                    tGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGtctc                             <  1:215684/69‑1 (MQ=255)
                                    tGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGtctc                             <  1:603184/69‑1 (MQ=255)
                                    tGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGtctc                             <  1:13987/69‑1 (MQ=255)
                                    tGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGtctc                             <  1:1362620/69‑1 (MQ=255)
                                    tGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGtctc                             <  1:2323172/69‑1 (MQ=255)
                                               ccGCGACATTCAGTGCAGCGCCATCCTCGCAAATGAtcatca                                             <  1:3145058/42‑1 (MQ=38)
                                                 gTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAg                <  1:503152/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACTGTCTCTACTAATACGCAGGgt             <  1:41236/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGgt             <  1:2755556/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGgt             <  1:486535/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGgt             <  1:3347395/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGgt             <  1:1131959/69‑1 (MQ=255)
                                                    aCATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGgt             <  1:2349985/69‑1 (MQ=255)
                                                         cAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAg         >  1:2407099/1‑68 (MQ=255)
                                                         cAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAg         >  1:1568045/1‑68 (MQ=255)
                                                         cAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAg         >  1:1587320/1‑68 (MQ=255)
                                                         cAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAg         >  1:2262525/1‑68 (MQ=255)
                                                              cAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAg    >  1:507253/1‑68 (MQ=255)
                                                              cAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAg    >  1:356298/1‑68 (MQ=255)
                                                              cAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAg    >  1:3319925/1‑68 (MQ=255)
                                                                gagCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAGGt  <  1:1550902/68‑1 (MQ=255)
                                                                gagCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAGGt  <  1:2123123/68‑1 (MQ=255)
                                                                gagCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAGGt  <  1:3308440/68‑1 (MQ=255)
                                                                 |                                                                  
TAAAGCTCACGTTAACGACCAGTTTGGCAACCCGGTTGCGCATCAACCCGTGACATTCAGTGCAGAGCCATCCTCGCAAATGATCATCAGCCAGAATACGGTCTCTACTAATACGCAGGGTGTAGCCGAGGT  >  minE/1283597‑1283728

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