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
A5 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,920,872 G→A T6I (ACA→ATA)  atpF ← F0 sector of membrane‑bound ATP synthase, subunit b

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,920,8720GA100.0% 209.0 / NA 60T6I (ACA→ATA) atpFF0 sector of membrane‑bound ATP synthase, subunit b
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (33/27);  total (33/27)

TGCTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTA  >  NC_000913/3920739‑3920987
                                                                                                                                     |                                                                                                                   
tgCTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCg                                                                                                                <  1:526507/139‑1 (MQ=255)
  cTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGtt                                                                                                              >  2:345580/1‑139 (MQ=255)
  cTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGtt                                                                                                              >  1:412348/1‑139 (MQ=255)
  cTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGtt                                                                                                              >  1:821196/1‑139 (MQ=255)
  cTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGtt                                                                                                              >  2:803612/1‑139 (MQ=255)
  cTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACATACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGtt                                                                                                              >  1:795108/1‑139 (MQ=255)
     gTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAg                                                                                                           <  1:628737/139‑1 (MQ=255)
               aGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGca                                                                                                 >  1:367031/1‑139 (MQ=255)
                  aaGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACaa                                                                                              <  2:706647/139‑1 (MQ=255)
                     gCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGc                                                                                           <  2:821196/139‑1 (MQ=255)
                             cAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTAttt                                                                                   <  1:275309/139‑1 (MQ=255)
                                   cTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTaa                                                                             <  2:367031/139‑1 (MQ=255)
                                       ttGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGtt                                                                         <  2:412348/139‑1 (MQ=255)
                                          aCGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTg                                                                      >  2:1006210/1‑139 (MQ=255)
                                                          gCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGAtt                                                                                                        >  2:798599/1‑89 (MQ=255)
                                                          gCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGAtt                                                                                                        <  1:798599/89‑1 (MQ=255)
                                                                      ggcCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCt                                          <  1:1006210/139‑1 (MQ=255)
                                                                       gcCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCtt                                         >  1:158193/1‑139 (MQ=255)
                                                                                      tGCAGAACTGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGa                          >  2:721669/1‑139 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                >  2:712471/1‑101 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                <  2:1080646/101‑1 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                >  1:1080646/1‑101 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                <  1:712471/101‑1 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCtt                                                           <  1:946491/106‑1 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCtt                                                           >  2:946491/1‑106 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGa                          >  2:553808/1‑139 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGa                          >  1:363069/1‑139 (MQ=255)
                                                                                      tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGa                          >  1:232410/1‑139 (MQ=255)
                                                                                          gaacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACAt                      <  2:363069/139‑1 (MQ=255)
                                                                                          gaacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACAt                      >  2:994182/1‑139 (MQ=255)
                                                                                           aacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTc                                                                        >  1:230945/1‑88 (MQ=255)
                                                                                           aacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTc                                                                        <  2:230945/88‑1 (MQ=255)
                                                                                           aacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                >  2:488805/1‑96 (MQ=255)
                                                                                           aacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTg                                                                <  1:488805/96‑1 (MQ=255)
                                                                                            acagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGatat                                                                  >  1:111971/1‑93 (MQ=255)
                                                                                            acagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGatat                                                                  <  2:111971/93‑1 (MQ=255)
                                                                                            acagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCa                    >  2:896020/1‑139 (MQ=255)
                                                                                                aacgaacAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACaa                                                                                              >  2:755486/1‑61 (MQ=255)
                                                                                                aacgaacAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACaa                                                                                              <  1:755486/61‑1 (MQ=255)
                                                                                                 acgaacAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAc               <  1:286376/139‑1 (MQ=255)
                                                                                                     acAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcagac           >  2:868720/1‑139 (MQ=255)
                                                                                                     acAGGACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcagac           >  1:365245/1‑139 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGtt                                                                               <  1:721383/68‑1 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGtt                                                                               >  2:721383/1‑68 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTc                                                                        >  1:473176/1‑75 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTc                                                                        <  2:473176/75‑1 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcagaccca        >  1:210439/1‑139 (MQ=255)
                                                                                                        ggACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcagaccca        <  2:795108/139‑1 (MQ=255)
                                                                                                         gACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGtt                                                                               >  2:925490/1‑67 (MQ=255)
                                                                                                         gACAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGtt                                                                               <  1:925490/67‑1 (MQ=255)
                                                                                                          aCAAACGCGATGGCCTGGCCG‑GGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGc                                                <  2:579160/96‑1 (MQ=255)
                                                                                                          aCAAACGCGATGGCCTGGCCG‑GGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGc                                                >  1:579160/1‑96 (MQ=255)
                                                                                                           cAAACGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcagacccagac     <  2:158193/139‑1 (MQ=255)
                                                                                                              aCGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcaga            >  1:376634/1‑129 (MQ=255)
                                                                                                              aCGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTAcaga            <  2:376634/129‑1 (MQ=255)
                                                                                                              aCGCGATGGCCTGGCCGAGGATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTa  >  1:307013/1‑139 (MQ=255)
                                                                                                                                ggATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTaa                                                                             >  1:396546/1‑46 (MQ=255)
                                                                                                                                ggATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTaa                                                                             <  2:396546/46‑1 (MQ=255)
                                                                                                                                ggATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCaa                                              >  1:1015801/1‑77 (MQ=255)
                                                                                                                                ggATTATTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCaa                                              <  2:1015801/77‑1 (MQ=255)
                                                                                                                                     |                                                                                                                   
TGCTCGTTCTGCGGAAGCAAGGCCGTCAGCAATTTCTTTTTGACGTTTTTCGATGGCTGCCATTAATGGCGGCCATACGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTA  >  NC_000913/3920739‑3920987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A