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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,569,847 C→T 23.1% P39P (CCC→CCT)  yibI → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,569,8470CT23.1% 310.0 / 85.8 164P39P (CCC→CCT) yibIpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (73/53);  new base T (19/19);  total (92/72)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.24e-01

Only 100 of 178 total aligned reads displayed.

GTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTG  >  minE/2569779‑2569916
                                                                    |                                                                     
gTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATcccc                                                                      <  1:2434928/70‑1 (MQ=255)
gTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATccc                                                                       <  1:2765947/69‑1 (MQ=255)
 tGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCAt                                                                    >  1:2705846/1‑71 (MQ=255)
   aTTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATg                                                                   <  1:4031945/70‑1 (MQ=255)
        ttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCg                                                                >  1:114063/1‑68 (MQ=255)
        ttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGAc                                                              >  1:5043405/1‑70 (MQ=255)
        ttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACg                                                             >  1:1469594/1‑71 (MQ=255)
        ttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACg                                                             >  1:797799/1‑71 (MQ=255)
           tGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                          <  1:2605352/71‑1 (MQ=255)
              aaTCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                                 <  1:1603628/61‑1 (MQ=255)
              aaTCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                                 <  1:4775917/61‑1 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTAt                                                         <  1:906763/67‑1 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                      >  1:3992792/1‑70 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCAt                                                     <  1:1797360/71‑1 (MQ=255)
                  atcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTAt                                                         <  1:2776419/65‑1 (MQ=255)
                  atcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                    >  1:1243472/1‑70 (MQ=255)
                   tcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACg                                                             >  1:1004806/1‑60 (MQ=255)
                   tcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcg                                                  >  1:3178585/1‑71 (MQ=255)
                    cgcgATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGa                                                               >  1:3722708/1‑57 (MQ=255)
                    cgcgATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTc                                                       >  1:1299216/1‑65 (MQ=255)
                    cgcgATACATGACATCCCTTATCTGATTGCAAAAAAGCGCAACCATCCCCATGCCGa                                                               >  1:1172349/1‑57 (MQ=255)
                     gcgATACATGACATCCCTTATCTGATTGCCAAAAAGAGCAACTATCCCCATGCCGACGCTATTCATAcggc                                                >  1:2421094/1‑71 (MQ=255)
                       gATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATccc                                                                       <  1:576693/46‑1 (MQ=255)
                         tACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGc                                                            <  1:2350146/55‑1 (MQ=255)
                         tACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                                <  1:2005412/67‑1 (MQ=255)
                           cATGATATTCCCTACCTGATTGCCAAAAAACGTAATCATCCTCATGCCGACg                                                             <  1:811494/52‑1 (MQ=255)
                           cATGATATTCCCTACCTGATTGCCAAAAAACGTAATCATCCTCATGCCGACg                                                             <  1:1092572/52‑1 (MQ=255)
                            aTGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                                 <  1:4485198/47‑1 (MQ=255)
                                  tCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                          <  1:700276/48‑1 (MQ=255)
                                  tCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                   <  1:4346774/71‑1 (MQ=255)
                                    ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGa                                                               >  1:3127835/1‑41 (MQ=255)
                                    ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCAt                                                     >  1:3402966/1‑51 (MQ=255)
                                    ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCAt                                                     >  1:4697492/1‑51 (MQ=255)
                                    ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCt                                 <  1:2332947/71‑1 (MQ=255)
                                      ttATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                          >  1:1282397/1‑44 (MQ=255)
                                      ttATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                          >  1:649719/1‑44 (MQ=255)
                                      ttATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGt                               >  1:2197050/1‑71 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGa                                                               >  1:3921082/1‑38 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACg                                                             <  1:2734561/40‑1 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTc                                                       >  1:1708686/1‑46 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTgg                                         <  1:3690337/60‑1 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                              >  1:3100864/1‑71 (MQ=255)
                                        accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              >  1:4671916/3‑70 (MQ=255)
                                        accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              >  1:4720228/3‑70 (MQ=255)
                                        accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              >  1:5464106/3‑70 (MQ=255)
                                        accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              >  1:1425786/3‑70 (MQ=255)
                                        accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              >  1:3829765/3‑70 (MQ=255)
                                        aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                          >  1:3741527/1‑42 (MQ=255)
                                        aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                      >  1:1366089/1‑46 (MQ=255)
                                        aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                              >  1:5463544/1‑70 (MQ=255)
                                         tCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcgg                                                 >  1:802442/1‑50 (MQ=255)
                                         ccTGATTGCCAAAAAACGTAATCATCCTCATGCCGa                                                               >  1:2995784/2‑36 (MQ=16)
                                         ccTGATTGCCAAAAAACGTAATCATCCTCATGCCGa                                                               >  1:831240/2‑36 (MQ=16)
                                         ccTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                              <  1:3537745/68‑1 (MQ=255)
                                          cTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTtttt                             <  1:4888679/69‑1 (MQ=255)
                                          cTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAc                           <  1:1573822/71‑1 (MQ=255)
                                           tGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTAtt                                                        <  1:4778394/41‑1 (MQ=255)
                                            gATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                         >  1:5291234/1‑69 (MQ=255)
                                             aTTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCa                                                      >  1:5217061/1‑41 (MQ=19)
                                              ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                        >  1:3853554/1‑70 (MQ=255)
                                              ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                       >  1:1663345/1‑71 (MQ=255)
                                               tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                       >  1:992449/1‑70 (MQ=255)
                                               tGCCAAAAAACGTAATCATCCTCATGCCGACGCCAtt                                                        >  1:2111344/1‑37 (MQ=16)
                                                gCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTa                            >  1:3065113/1‑64 (MQ=255)
                                                  cAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATg                   >  1:4926543/1‑71 (MQ=255)
                                                   aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                  >  1:3214145/1‑71 (MQ=255)
                                                   aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                  >  1:660056/1‑71 (MQ=255)
                                                   aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                  >  1:1269569/1‑71 (MQ=255)
                                                    aaaaGCGCAACCATCCCCATGCCGACGCTATTCAt                                                     <  1:2710445/35‑1 (MQ=255)
                                                    aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTa                            >  1:5133009/1‑60 (MQ=255)
                                                    aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                  >  1:435764/1‑70 (MQ=255)
                                                    aaaaGCGCAACCATCCCCAAGCCGACGCTATTCATAcggcgg                                              >  1:2823040/1‑42 (MQ=255)
                                                    aaaaACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                  >  1:4942626/1‑70 (MQ=255)
                                                      aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTgg                                         >  1:2292439/1‑45 (MQ=255)
                                                      aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt               >  1:1164799/1‑71 (MQ=255)
                                                       aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc              <  1:5631368/71‑1 (MQ=255)
                                                       aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc              <  1:22948/71‑1 (MQ=255)
                                                            aaCCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc              <  1:3414335/66‑1 (MQ=255)
                                                              tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                <  1:2660539/61‑1 (MQ=255)
                                                              tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                <  1:768040/61‑1 (MQ=255)
                                                              tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                <  1:5340909/61‑1 (MQ=255)
                                                              tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTAt               >  1:3518308/2‑63 (MQ=255)
                                                              tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGt       <  1:1009023/70‑1 (MQ=255)
                                                              ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt       <  1:4374643/71‑1 (MQ=255)
                                                              ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt       <  1:515595/71‑1 (MQ=255)
                                                              ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt       <  1:2571623/71‑1 (MQ=255)
                                                               cATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                  >  1:2114441/1‑59 (MQ=255)
                                                                aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGtt                 >  1:3210049/1‑59 (MQ=255)
                                                                aTCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGttt     <  1:5020467/71‑1 (MQ=255)
                                                                aTCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGtt      >  1:4722256/1‑70 (MQ=255)
                                                                 tCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                         <  1:1721333/50‑3 (MQ=255)
                                                                 tCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                         <  1:2048407/50‑3 (MQ=255)
                                                                 tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                              <  1:2935852/45‑1 (MQ=255)
                                                                 tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc    <  1:1489890/71‑1 (MQ=255)
                                                                 tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc    <  1:1196356/71‑1 (MQ=255)
                                                                   cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtg  <  1:2724093/71‑1 (MQ=255)
                                                                   cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt   <  1:3068120/70‑1 (MQ=255)
                                                                   cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt   <  1:3899699/70‑1 (MQ=255)
                                                                   cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt   >  1:4563581/1‑70 (MQ=255)
                                                                   cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt   <  1:1131859/70‑1 (MQ=255)
                                                                    |                                                                     
GTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTG  >  minE/2569779‑2569916

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