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 1,775,995 C→A 36.7% I309I (ATC→ATA)  yfiN → predicted diguanylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,775,9950CA36.7% 85.5 / 74.4 98I309I (ATC→ATA) yfiNpredicted diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base C (52/10);  new base A (13/23);  total (65/33)
Fisher's exact test for biased strand distribution p-value = 2.22e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01

Only 100 of 119 total aligned reads displayed.

AATTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGC  >  minE/1775933‑1776063
                                                              |                                                                    
aaTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCaaaa                                                                >  1:2280817/1‑69 (MQ=255)
aaTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCaaaa                                                                >  1:2466451/1‑69 (MQ=255)
aaTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCaaaa                                                                >  1:2984382/1‑69 (MQ=255)
aaTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCaaaa                                                                >  1:1332565/1‑69 (MQ=255)
aaTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCaaaa                                                                >  1:2964702/1‑69 (MQ=255)
 aTTTCAAATATATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATAGCaaaa                                                                >  1:2458168/1‑68 (MQ=255)
 aTTTCAAATATATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAAc                                                               >  1:2234095/1‑69 (MQ=255)
 aTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAAc                                                               >  1:2315585/1‑69 (MQ=255)
 aTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAAc                                                               >  1:332603/1‑69 (MQ=255)
 aTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAAc                                                               >  1:3274124/1‑69 (MQ=255)
 aTTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAAc                                                               >  1:3101932/1‑69 (MQ=255)
   ttCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACg                                                              >  1:982388/1‑68 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACgtt                                                            <  1:3412721/69‑3 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACg                                                              >  1:3094738/1‑67 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGt                                                            <  1:664067/69‑1 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGt                                                            <  1:673211/69‑1 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGt                                                            <  1:1035138/69‑1 (MQ=255)
    tCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTAATTGAAATCGCAAAACGGt                                                            <  1:3089035/69‑1 (MQ=255)
     cAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGt                                                            <  1:2920645/68‑1 (MQ=255)
          aCATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTg                                                      >  1:1298158/1‑69 (MQ=255)
          aCATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTg                                                      >  1:2703207/1‑69 (MQ=255)
          aCATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTg                                                      >  1:299643/1‑69 (MQ=255)
           cATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTT‑GCTGaa                                                    >  1:289444/1‑69 (MQ=255)
           cATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTT‑GCTGaa                                                    >  1:1656651/1‑69 (MQ=255)
               aaTGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAAttt                                                 >  1:1004920/1‑69 (MQ=255)
               aaTGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAAttt                                                 >  1:1225562/1‑69 (MQ=255)
               aaTGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAAttt                                                 >  1:443249/1‑69 (MQ=255)
               aaTGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAAttt                                                 >  1:188041/1‑69 (MQ=255)
               aaTGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAAttt                                                 >  1:923551/1‑69 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1549440/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1423167/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:3036837/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:2392416/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1818417/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:968403/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:2320843/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:167584/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:2312889/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:2275078/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:222591/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:3308781/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1146982/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1658740/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:2071276/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:487913/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1914252/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:595939/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1113913/45‑1 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTg                                                >  1:1859847/1‑54 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:1456138/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:1369367/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:2725222/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:3186315/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:2355971/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:1216189/1‑67 (MQ=255)
                               aTGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACa                                   >  1:700617/1‑67 (MQ=255)
                                tGCGACGGGCGATAGAGTCTTGATTGAAATAGCAAAACGGTTAg                                                         <  1:1393485/44‑1 (MQ=255)
                                        tcGATAGAGTCTTGATTGAAATAGCATAACGGTTAg                                                         <  1:186026/35‑1 (MQ=37)
                                             agagTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTg                   >  1:1790780/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTTCGACATAAAGCATACCGCCTGggc                >  1:1618005/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTggg                 >  1:2028434/1‑68 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:1568260/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:789425/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:1884369/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:237414/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:405903/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:285800/1‑69 (MQ=255)
                                                gTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggc                >  1:3247603/1‑69 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             >  1:356384/1‑69 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             >  1:1818579/1‑69 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             <  1:426995/69‑1 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             >  1:1456358/1‑69 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             >  1:2567343/1‑69 (MQ=255)
                                                   ttgattgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGggcggc             >  1:243225/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATg         <  1:532159/68‑1 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATg         >  1:1772879/1‑68 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:1852733/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:187140/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:1100880/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:2115322/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:1260975/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:212490/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGa        >  1:75618/1‑69 (MQ=255)
                                                        tgaAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGAATACCGCCTGGGCGGCGATGa        >  1:2793641/1‑69 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:3003397/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:690358/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:714480/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:2812650/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:2943099/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:530509/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:2358725/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:456985/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:414807/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:3101649/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:3379976/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:2199106/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:2203325/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:3283076/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:1250285/69‑1 (MQ=255)
                                                              cGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGc  <  1:316735/69‑1 (MQ=255)
                                                              |                                                                    
AATTTCAAATACATCAATGATACCTGGGGTCATGCGACGGGCGATAGAGTCTTGATTGAAATCGCAAAACGGTTAGCTGAATTTGGCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCGATGAATTCGC  >  minE/1775933‑1776063

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