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
A9 F28 I1 R1	120	56.0	1898522	99.4%	1887130	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,539,616	C→T	intergenic (‑115/‑1341)	nanC ← / → fimB	N‑acetylneuraminic acid outer membrane channel/regulator for fimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,539,616	0	C	T	100.0%	178.4 / NA	51	intergenic (‑115/‑1341)	nanC/fimB	N‑acetylneuraminic acid outer membrane channel/regulator for fimA
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (22/29); total (22/29)

AAAGTATTTTAGCCTTTTTCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAG  >  NC_000913/4539480‑4539750

aaaGTATTTTAGCCTTTTTCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGt                                                                                                                                     >  1:571820/1‑140 (MQ=255)

         tAGCCTTTTTCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTatat                                                                                                                            >  2:750755/1‑140 (MQ=255)

             cTTTTTCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATAttttt                                                                                                                        <  1:464049/140‑1 (MQ=255)

              tttttCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATAtttttt                                                                                                                       >  1:890928/1‑140 (MQ=255)

                      aaaTTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAg                                                                                                               <  1:837994/140‑1 (MQ=255)

                        aTTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGt                                                                                                             <  1:163553/140‑1 (MQ=255)

                        aTTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGt                                                                                                             <  2:571820/140‑1 (MQ=255)

                        aTTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGt                                                                                                             <  2:780426/140‑1 (MQ=255)

                                   ttGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGaaa                                                                                                  >  1:425295/1‑140 (MQ=255)

                                   ttGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGaaa                                                                                                  <  1:23774/140‑1 (MQ=255)

                                           tACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCtt                                                                                          >  1:586502/1‑140 (MQ=255)

                                            aCAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCttt                                                                                         >  2:423730/1‑140 (MQ=255)

                                               gAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTca                                                                                      <  2:890928/140‑1 (MQ=255)

                                                aaaGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTcac                                                                                     >  1:212085/1‑140 (MQ=255)

                                                aaaGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTcac                                                                                     <  1:763098/140‑1 (MQ=255)

                                                  aGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATA‑TTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACatt                                                                                  >  1:338420/1‑140 (MQ=255)

                                                      aTACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACattatt                                                                               <  1:24947/140‑1 (MQ=255)

                                                       tACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGGAAAATCTCTTTTCACATTAttt                                                                              >  1:637209/1‑140 (MQ=255)

                                                       tACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTAttt                                                                              >  1:812983/1‑140 (MQ=255)

                                                              cccGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTtaaataaa                                                                       >  1:842235/1‑140 (MQ=255)

                                                                   aTAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACagag                                                                  >  2:857081/1‑140 (MQ=255)

                                                                   aTAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACa                                                                     <  1:640550/137‑1 (MQ=255)

                                                                   aTAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACa                                                                     >  2:640550/1‑137 (MQ=255)

                                                                          aTTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGa                                                           <  2:198432/140‑1 (MQ=255)

                                                                             aGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTa                                                        >  1:897916/1‑140 (MQ=255)

                                                                                  ttATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATAc                                                   <  1:886020/140‑1 (MQ=255)

                                                                                    aTGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATATAAATAAACAGAGATCCAGATTAAATACCt                                                 <  2:625279/140‑1 (MQ=255)

                                                                                     tgttgtGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTg                                                <  2:842235/140‑1 (MQ=255)

                                                                                      gttgtGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGa                                               >  2:298609/1‑140 (MQ=255)

                                                                                         gtgtAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGta                                            >  2:769864/1‑140 (MQ=255)

                                                                                         gtgtAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGta                                            >  2:358986/1‑140 (MQ=255)

                                                                                            tAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATaa                                         >  2:360747/1‑140 (MQ=255)

                                                                                                  ttttttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAAtctc                                   <  1:360747/140‑1 (MQ=255)

                                                                                                     tttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCtcttc                                <  2:946517/140‑1 (MQ=255)

                                                                                                     tttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCtcttc                                <  1:750755/140‑1 (MQ=255)

                                                                                                       tGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTg                              <  1:298609/140‑1 (MQ=255)

                                                                                                                tataGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAAt                     <  2:338420/140‑1 (MQ=255)

                                                                                                                tataGTGTCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAAt                     <  1:673385/140‑1 (MQ=255)

                                                                                                                      gtCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGAttt               <  1:788930/140‑1 (MQ=255)

                                                                                                                       tCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTg              >  1:171418/1‑140 (MQ=255)

                                                                                                                       tCTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTg              >  2:892704/1‑140 (MQ=255)

                                                                                                                        cTTTGGCAACCGGTAGTTGTATTTTATATTTTTTTGGATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTTATTGATTTGa             >  2:186301/1‑140 (MQ=255)

                                                                                                                         tttGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGaa            <  2:586502/140‑1 (MQ=255)

                                                                                                                          ttGGCAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAAt           <  2:812983/140‑1 (MQ=255)

                                                                                                                              cAACCGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTc       <  2:171418/140‑1 (MQ=255)

                                                                                                                                 ccGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTa    <  1:769864/140‑1 (MQ=255)

                                                                                                                                 ccGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTa    <  1:423730/140‑1 (MQ=255)

                                                                                                                                 ccGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTa    <  1:857081/140‑1 (MQ=255)

                                                                                                                                 ccGGTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTa    <  2:212085/140‑1 (MQ=255)

                                                                                                                                   ggTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAg  <  1:358986/140‑1 (MQ=255)

                                                                                                                                   ggTAGTTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAg  >  1:939272/1‑140 (MQ=255)

AAAGTATTTTAGCCTTTTTCATAAATTTCACTCATTTGTAGGATACAGAAAGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCTTTTCACATTATTTAAATAAACAGAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAG  >  NC_000913/4539480‑4539750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A