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 R2 251 90.0 5200563 86.9% 4519289 59.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,595,761 G→T 12.0% P279P (CCC→CCA)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,7610GT12.0% 239.9 / 12.9 75P279P (CCC→CCA) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (31/35);  new base T (6/3);  total (37/38)
Fisher's exact test for biased strand distribution p-value = 3.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

GGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATC  >  minE/2595701‑2595827
                                                            |                                                                  
ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                          <  1:2963143/71‑1 (MQ=255)
ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                          <  1:4911483/71‑1 (MQ=255)
ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                          <  1:2506876/71‑1 (MQ=255)
ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                          <  1:4508988/71‑1 (MQ=255)
ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                          <  1:736425/71‑1 (MQ=255)
      gcgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAgg                                                     >  1:4477667/1‑70 (MQ=255)
      gcgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                    >  1:4760159/1‑71 (MQ=255)
      gcgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                    >  1:4208516/1‑71 (MQ=255)
       cgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGAc                                                   >  1:3986230/1‑71 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCTAGGGGGCACCGCGCAGGACTTTACCCg                                           >  1:1994388/1‑70 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:1640059/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:4425164/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:1114187/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:1805366/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:1278359/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:1871839/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:3025739/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                             <  1:5053945/52‑1 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTAccc                                            >  1:3169769/1‑69 (MQ=255)
                tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCg                                           >  1:302012/1‑70 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:2717454/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:3203780/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:3652204/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:1564081/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:728254/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:1855670/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                   >  1:4245624/1‑44 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTa                                         <  1:489454/70‑1 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTAt                                        >  1:3996750/1‑71 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTAt                                        >  1:1811029/1‑71 (MQ=255)
                  aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTAt                                        >  1:824228/1‑71 (MQ=255)
                         aGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                                  >  1:471589/1‑70 (MQ=255)
                         aGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGc                                 <  1:4850556/71‑1 (MQ=255)
                          gATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCa                                <  1:5047097/71‑1 (MQ=255)
                            tACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATg                              <  1:3809251/71‑1 (MQ=255)
                            tACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATg                              <  1:3476054/71‑1 (MQ=255)
                            tACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATg                              <  1:4321383/71‑1 (MQ=255)
                            tACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGAAt                               <  1:196274/70‑1 (MQ=255)
                             aCATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGa                             >  1:1059677/1‑71 (MQ=255)
                             aCATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGa                             >  1:2745877/1‑71 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:2969399/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:4496596/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:1613584/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:2365532/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:565496/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:2449413/1‑38 (MQ=255)
                               aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                            >  1:4860973/1‑38 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTccg                                            >  1:4369955/1‑52 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcct                          >  1:2643713/1‑70 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcct                          >  1:4590037/1‑70 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcct                          >  1:3760988/1‑70 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcct                          >  1:2363060/1‑70 (MQ=255)
                                tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcc                           >  1:2919275/1‑70 (MQ=255)
                                      gtgagaAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCttttc                    <  1:2800717/69‑2 (MQ=255)
                                      gtgagaAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCttttc                    <  1:3026550/69‑2 (MQ=255)
                                      gtgagaAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCttttc                    <  1:4383066/69‑2 (MQ=255)
                                        gagaAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                                  <  1:1917654/55‑1 (MQ=255)
                                        gagaAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                                  <  1:4328686/55‑1 (MQ=255)
                                        gagaAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGc                  <  1:1119414/71‑1 (MQ=255)
                                         agaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                      <  1:2224188/50‑1 (MQ=255)
                                         agaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                      <  1:786577/50‑1 (MQ=255)
                                          gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCa                                >  1:1095870/1‑55 (MQ=255)
                                          gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCa                                >  1:2173623/1‑55 (MQ=255)
                                          gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCa                                >  1:3299263/1‑55 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                        <  1:414333/62‑1 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                        <  1:3610010/62‑1 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                        <  1:3255475/62‑1 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                        <  1:2933304/62‑1 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                        <  1:5078090/62‑1 (MQ=255)
                                           aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCCTATTAATCGCATGACcgcg                        <  1:728229/62‑1 (MQ=255)
                                            agaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTaa                                     >  1:2548385/1‑48 (MQ=255)
                                             gaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                      >  1:4425836/1‑62 (MQ=255)
                                               tGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa           <  1:3021015/71‑1 (MQ=255)
                                                gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa           >  1:4341645/1‑70 (MQ=255)
                                                gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa           >  1:1406680/1‑70 (MQ=255)
                                                gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa           >  1:3648213/1‑70 (MQ=255)
                                                 aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGa                             >  1:1650575/1‑51 (MQ=255)
                                                 aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGAc                            >  1:5147509/1‑52 (MQ=255)
                                                 aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaa          <  1:1789208/70‑1 (MQ=255)
                                                       tGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcgacga             >  1:367128/1‑61 (MQ=255)
                                                         ccAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                                  <  1:2629714/38‑1 (MQ=255)
                                                         ccAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATc  <  1:2419454/70‑1 (MQ=255)
                                                            |                                                                  
GGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATC  >  minE/2595701‑2595827

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A