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 303,976 A→T 35.3% P43P (CCA→CCT)  ybaY → predicted outer membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE303,9760AT35.3% 87.4 / 80.1 99P43P (CCA→CCT) ybaYpredicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (34/30);  new base T (7/28);  total (41/58)
Fisher's exact test for biased strand distribution p-value = 1.45e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAGCGCGGATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGA  >  minE/303911‑304041
                                                                 |                                                                 
aaaaGCGCGGATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGc                                                                 <  1:2974608/68‑1 (MQ=255)
 aaaGCGCGGATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTa                                                               >  1:2998097/1‑69 (MQ=255)
 aaaGCGCGGATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTa                                                               >  1:1438514/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:209330/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:997051/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:2071125/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:235378/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:2398135/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCTGCTATCCAGCa                                                        >  1:2453390/1‑69 (MQ=255)
        ggATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAACAACACAACAACCTGCTATCCAGc                                                         >  1:2834150/1‑68 (MQ=255)
             ttCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGa                                                   <  1:2333267/69‑1 (MQ=255)
             ttCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGa                                                   <  1:2754209/69‑1 (MQ=255)
             ttCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGa                                                   <  1:3362129/69‑1 (MQ=255)
              tCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGa                                                   <  1:927976/68‑1 (MQ=255)
                        gCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGt                                        <  1:2658484/69‑1 (MQ=255)
                          aCCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTAc                                      >  1:998233/1‑69 (MQ=255)
                          aCCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTAc                                      >  1:1253413/1‑69 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:360607/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:1126288/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:894952/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:1853084/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:2781563/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:1277740/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:652733/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:319706/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:3173687/67‑1 (MQ=255)
                                    aaTACGTCTATTTCAGAAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGa                              <  1:1143169/67‑1 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:154634/1‑68 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1738012/1‑68 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:309863/1‑68 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1234915/1‑68 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:882990/1‑68 (MQ=255)
                                      tACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:2022393/1‑68 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAg                                                          >  1:275153/1‑36 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:2530611/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:874649/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:884479/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:271248/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:2773359/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1412928/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1651648/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:146782/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1931956/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATcc                           >  1:1232952/1‑67 (MQ=255)
                                       aCGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCT‑‑GGTACCGTCTGGATCCGTc                        >  1:731874/1‑68 (MQ=255)
                                         gTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTATCCGGTACCGTCTGGa                              <  1:2440078/62‑1 (MQ=255)
                                            tATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACGGTCTGGATCCGTCa                       >  1:534549/1‑66 (MQ=255)
                                                  aGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCg               <  1:1136099/68‑1 (MQ=255)
                                                   gCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCg               <  1:377275/67‑1 (MQ=255)
                                                   gCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGc              <  1:1504960/68‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:3406731/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1542306/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:290869/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1476867/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:3015100/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:961361/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1447164/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:3233423/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1424771/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1160640/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1057705/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:443107/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1341427/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1267659/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2722388/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1932365/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2556817/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2623785/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2436842/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2716327/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2046001/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1748026/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:22183/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2755731/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2198813/69‑1 (MQ=255)
                                                    caacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:2787584/69‑1 (MQ=255)
                                                     aacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:1224574/68‑1 (MQ=255)
                                                     aacacaacaACCTGCTATCCAGCAACCGAATGTCTCCGGTACCGTTTGGATCCGTCAGAAAGTCGCAc            <  1:399240/68‑1 (MQ=255)
                                                        acaacaACCAGCTATCCAGCAACCGAATGTCTCCg                                          >  1:968041/1‑35 (MQ=255)
                                                        acaacaACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgcc        >  1:2766715/1‑69 (MQ=255)
                                                        acaacaACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgcc        <  1:625711/69‑1 (MQ=255)
                                                        acaacaACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgcc        <  1:2664248/69‑1 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:208318/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:2181245/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:561802/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:1004710/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:347689/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:1896469/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:1747145/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgccgc      >  1:2823839/1‑68 (MQ=255)
                                                           acaacCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTgcc        >  1:280072/1‑66 (MQ=255)
                                                              acCAGCTATCCAGTAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:2325156/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:3338033/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:1988961/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:1434170/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:2724072/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:3059122/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:1161153/69‑1 (MQ=255)
                                                              acCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGa  <  1:1656218/69‑1 (MQ=255)
                                                                 |                                                                 
AAAAGCGCGGATATTCAGACGCCAGCACCGGCTGCAAATACGTCTATTTCAGCAACACAACAACCAGCTATCCAGCAACCGAATGTCTCCGGTACCGTCTGGATCCGTCAGAAAGTCGCACTGCCGCCTGA  >  minE/303911‑304041

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