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
A7 F28 I1 R1 252 48.5 1661298 98.8% 1641362 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,428,493 T→C noncoding (270/1542 nt) rrsD ← 16S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,428,4930TC97.6% 99.8 / ‑4.5 42noncoding (270/1542 nt)rrsD16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (22/19);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01

GTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGG  >  NC_000913/3428418‑3428628
                                                                           |                                                                                                                                       
gTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAggg                                                                         <  1:302918/140‑1 (MQ=17)
  aGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTc                                                                       <  1:158067/140‑1 (MQ=18)
  aGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTc                                                                       <  1:474203/140‑1 (MQ=18)
                tgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCt                                                         >  1:567024/1‑140 (MQ=17)
                tgtCTCAGTTCCAGTGGGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGACCCCCTCTTTGGTCt                                                         >  2:161850/1‑140 (MQ=12)
                     cAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCTCTCTTTGGTCTTGCGa                                                    >  2:614022/1‑140 (MQ=17)
                       gTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACg                                                  <  1:344313/140‑1 (MQ=18)
                       gTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACg                                                  <  2:717670/140‑1 (MQ=18)
                            ggtgtGGCTGATCTTCCTCACAGACAAGCTAGGGACCGCCGCGTTGGCGAGCCGTTCCCCCACCAACAAGCTAAGCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  2:447408/139‑1 (MQ=11)
                            aGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  2:50158/140‑1 (MQ=35)
                            aGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  1:410020/140‑1 (MQ=25)
                            aGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  1:450593/140‑1 (MQ=25)
                            aGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  2:779909/140‑1 (MQ=25)
                                tgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGt                                         <  2:567024/140‑1 (MQ=25)
                                      gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACg                                                  >  2:430400/1‑125 (MQ=18)
                                      gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACg                                                  <  1:430400/125‑1 (MQ=21)
                                      gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             >  1:755946/1‑130 (MQ=25)
                                      gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  2:755946/130‑1 (MQ=25)
                                        cATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTa                                 <  2:167392/140‑1 (MQ=25)
                                          tcctccCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             <  2:700934/126‑1 (MQ=255)
                                          tCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATg                                             >  1:700934/1‑126 (MQ=25)
                                          tCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTAcc                               <  2:530345/140‑1 (MQ=25)
                                              ctcAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTAcc                               <  2:291754/136‑1 (MQ=25)
                                              ctcAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTAcc                               >  1:291754/1‑136 (MQ=21)
                                              ctcAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGttt                           >  2:340572/1‑140 (MQ=21)
                                                cAGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTcc                         >  2:776683/1‑140 (MQ=21)
                                                 aGACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCa                        <  1:340572/140‑1 (MQ=25)
                                                  gACCAGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCag                       <  2:248618/140‑1 (MQ=25)
                                                      aGCTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCagtagt                   <  1:122909/140‑1 (MQ=25)
                                                        cTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTa                 <  2:9967/140‑1 (MQ=21)
                                                        cTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTa                 >  1:60178/1‑140 (MQ=21)
                                                        cTAGGGATCGTCGCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTa                 >  1:9967/1‑140 (MQ=21)
                                                                cgtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTc         >  1:356198/1‑140 (MQ=21)
                                                                 gtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCt          <  1:611773/138‑1 (MQ=21)
                                                                 gtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCt          >  2:611773/1‑138 (MQ=21)
                                                                 gtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTcc        >  2:249845/1‑140 (MQ=21)
                                                                 gtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTcc        >  2:701494/1‑140 (MQ=21)
                                                                 gtcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTcc        >  2:461411/1‑140 (MQ=21)
                                                                  tcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa       >  2:561355/1‑140 (MQ=21)
                                                                  tcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa       >  2:421229/1‑140 (MQ=21)
                                                                  tcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa       >  2:764947/1‑140 (MQ=21)
                                                                  tcgCCTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGGCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa       >  2:496312/1‑140 (MQ=21)
                                                                     ccTTGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCa    >  1:188680/1‑140 (MQ=21)
                                                                       ttGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAgg  >  1:526629/1‑140 (MQ=21)
                                                                       ttGGCGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAgg  <  1:461411/140‑1 (MQ=21)
                                                                           |                                                                                                                                       
GTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCATCAGG  >  NC_000913/3428418‑3428628

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A