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
A3 F2 I1 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 Exported 704,300 G→A 21.1% R115R (CGC→CGT)  ymcA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported704,3000GA21.1% 213.2 / 46.9 104R115R (CGC→CGT) ymcAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (42/40);  new base A (10/12);  total (52/52)
Fisher's exact test for biased strand distribution p-value = 8.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

Only 100 of 105 total aligned reads displayed.

CAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCACTGGCTAT  >  Exported/704231‑704367
                                                                     |                                                                   
cAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGc                                                                    >  1:2162574/1‑71 (MQ=255)
       gTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGtt                                                              >  1:4853548/1‑70 (MQ=255)
          ccAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGaa                                                                 >  1:1735024/1‑64 (MQ=255)
           cAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                                          <  1:4148528/70‑1 (MQ=255)
            aGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGaa                                                                 >  1:2754284/1‑62 (MQ=255)
                 tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                                                   <  1:4213472/55‑1 (MQ=255)
                 tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                                                   <  1:138198/55‑1 (MQ=255)
                  atCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                                                    >  1:2059709/1‑69 (MQ=255)
                   tCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                                           <  1:5641687/61‑1 (MQ=255)
                   tCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAAt                                                   >  1:4654760/1‑69 (MQ=255)
                     aCGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                                        >  1:2205433/1‑62 (MQ=255)
                     aCGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAtt                                               >  1:4414167/1‑71 (MQ=255)
                     aCGTTTACCAAACGCAACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                                        >  1:3409610/1‑62 (MQ=255)
                      cGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAgg                                                                     <  1:473230/48‑1 (MQ=255)
                       gTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                                                   <  1:2419561/49‑1 (MQ=255)
                       gTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTg                                             >  1:2473338/1‑71 (MQ=255)
                        tttACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGa                                                                  <  1:2828585/49‑1 (MQ=255)
                         ttACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaaa                                                         >  1:311831/1‑57 (MQ=255)
                          tACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAttt                                              <  1:4087923/67‑1 (MQ=255)
                           aCCAACCGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCtt                                         <  1:5372011/71‑1 (MQ=255)
                            ccAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCtt                                         <  1:2763889/70‑1 (MQ=255)
                             cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaaa                                                         >  1:3623456/1‑53 (MQ=255)
                             cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAttt                                              <  1:4834842/64‑1 (MQ=255)
                             cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:4194489/71‑1 (MQ=255)
                             cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:2303699/71‑1 (MQ=255)
                              aaaCGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGt                                      <  1:5401449/71‑1 (MQ=255)
                               accgcgACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTtata                                     >  1:4471478/3‑71 (MQ=255)
                               accGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTtata                                     >  1:3816527/3‑71 (MQ=255)
                                ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             <  1:2811956/45‑1 (MQ=16)
                                ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             <  1:5020055/45‑1 (MQ=16)
                                ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             <  1:4133729/45‑1 (MQ=16)
                                ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             <  1:1650483/45‑1 (MQ=16)
                                ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             <  1:1437401/45‑1 (MQ=16)
                                 cGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGATTGATTTGTCTTTGTATg                                   <  1:2826470/71‑1 (MQ=255)
                                  gCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                                             >  1:3198555/1‑44 (MQ=16)
                                   ccACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGtt                                                              >  1:5680876/1‑42 (MQ=16)
                                     aCTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTg                               <  1:298368/71‑1 (MQ=255)
                                      cTTGCGGTAGCCAGTAACCTTCTTCCCAGAGGCGAAGttt                                                             >  1:5490348/1‑40 (MQ=255)
                                      cTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGttt                                                             >  1:5004219/1‑40 (MQ=255)
                                      cTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGa                              <  1:4845245/71‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                                          <  1:603560/42‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                                          <  1:4581591/42‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                                           <  1:2062117/41‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                                           <  1:1533551/41‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                                           <  1:279047/41‑1 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                                        >  1:1376976/1‑60 (MQ=255)
                                       ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                                        >  1:2282672/1‑60 (MQ=255)
                                       ttGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATc                                           <  1:4057529/57‑1 (MQ=255)
                                        tGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCt                                          >  1:3091942/1‑57 (MQ=255)
                                        tGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATc                            >  1:1750856/1‑71 (MQ=255)
                                        tGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATc                            >  1:3675203/1‑71 (MQ=255)
                                        tGCGGCAGCCAGTAACTCACTTCCCACAAACGCAGATTGAGATCGAAGGCTTTATCTTtata                                     >  1:3758542/1‑62 (MQ=255)
                                         gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                                        >  1:4923259/1‑42 (MQ=255)
                                         gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                                        >  1:570752/1‑42 (MQ=255)
                                         gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                                        >  1:5088302/1‑42 (MQ=255)
                                         gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                                                    >  1:3399473/1‑46 (MQ=255)
                                         gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                                                    >  1:1240711/1‑46 (MQ=255)
                                          cGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATcg                           <  1:2704464/70‑1 (MQ=255)
                                          cGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATcgc                          <  1:3651759/71‑1 (MQ=255)
                                          cGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATcgc                          <  1:4096640/71‑1 (MQ=255)
                                             tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:1648098/55‑1 (MQ=255)
                                             tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:1210079/55‑1 (MQ=255)
                                             tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:2474168/55‑1 (MQ=255)
                                             tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg                                       <  1:4445834/55‑1 (MQ=255)
                                                  aGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCttta                                       >  1:1135682/1‑49 (MQ=255)
                                                  aGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCttta                                       >  1:1501238/1‑49 (MQ=255)
                                                  aGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGaaa                  <  1:2124752/71‑1 (MQ=255)
                                                  aGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGaaa                  <  1:2746868/71‑1 (MQ=255)
                                                   gTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCttta                                             <  1:5629868/43‑2 (MQ=255)
                                                   gTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCttta                                             <  1:4888498/43‑2 (MQ=255)
                                                   gTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCttta                                             <  1:3257370/43‑2 (MQ=255)
                                                   gTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAAt                 <  1:3557014/71‑1 (MQ=255)
                                                   gTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCAGAAAt                 <  1:2269246/71‑1 (MQ=255)
                                                    tAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                                        <  1:5454464/47‑1 (MQ=255)
                                                    tAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                                        <  1:1188925/47‑1 (MQ=255)
                                                    tAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                                        <  1:4772255/47‑1 (MQ=255)
                                                    tAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGaa                   >  1:130526/1‑68 (MQ=255)
                                                    tAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGaa                   >  1:1528892/1‑68 (MQ=255)
                                                     aaCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACt                                >  1:1236879/1‑54 (MQ=255)
                                                     aaCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACt                                >  1:3500166/1‑54 (MQ=255)
                                                     aaCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCt               >  1:1163262/1‑71 (MQ=255)
                                                      aCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAttt                                              >  1:2115823/1‑39 (MQ=255)
                                                      aCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGt                                      >  1:5538718/1‑47 (MQ=255)
                                                      aCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCtt              >  1:1807894/1‑71 (MQ=255)
                                                      aCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCtt              >  1:3100519/1‑71 (MQ=255)
                                                      aCCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCt               >  1:4132175/1‑70 (MQ=255)
                                                        cttcttCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTcc            >  1:4450791/1‑71 (MQ=255)
                                                         ttcttcCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAAt                 >  1:3540141/1‑65 (MQ=255)
                                                         ttcttcCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCAGCTGAAATCTTcc            >  1:2706530/1‑70 (MQ=255)
                                                          tcttcCCACAGGCGAAGTTTAAAATCGAGTGAttt                                              <  1:2149124/35‑1 (MQ=255)
                                                           cttcCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCAc         >  1:4357608/1‑71 (MQ=255)
                                                           cttcCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCAc         >  1:3531913/1‑71 (MQ=255)
                                                            ttcCCACAGGCGAATTTTAAAATCGAATGATTTGTCTTTg                                       <  1:1648101/40‑1 (MQ=255)
                                                                 acaGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTa                                     >  1:822542/1‑37 (MQ=255)
                                                                 acaGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTAt                                    <  1:2463480/38‑1 (MQ=255)
                                                                 acaGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGaa                   <  1:4293144/55‑1 (MQ=255)
                                                                 acaGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCACTGGCta   >  1:428365/1‑71 (MQ=255)
                                                                  caGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGGTGAAATCTTCCCACTGGc     <  1:4277656/68‑1 (MQ=255)
                                                                  caGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAAt                 >  1:875528/1‑56 (MQ=255)
                                                                  caGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCACTGGCtat  <  1:1734292/71‑1 (MQ=255)
                                                                     |                                                                   
CAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGCCGCTGAAATCTTCCCACTGGCTAT  >  Exported/704231‑704367

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