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	1,712,518	(C)_6→7	intergenic (+360/‑251)	nth → / → dtpA	endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,712,512	1	.	C	92.7%	134.8 / 3.6	41	intergenic (+354/‑257)	nth/dtpA	endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA
Reads supporting (aligned to +/- strand): ref base . (0/3); new base C (26/12); total (26/15)
Fisher's exact test for biased strand distribution p-value = 4.27e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

AGAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGA  >  NC_000913/1712373‑1712645

aGAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑Ca                                                                                                                                        <  1:825720/140‑1 (MQ=255)

  aaTCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑cc                                                                                                                                     <  2:158883/140‑1 (MQ=255)

   aTCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTATACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑ccc                                                                                                                                    >  1:432644/1‑140 (MQ=255)

   aTCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑ccc                                                                                                                                    <  2:318652/140‑1 (MQ=255)

     cAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑ccccc                                                                                                                                  <  1:166783/140‑1 (MQ=255)

                  tttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTcagtgcag                                                                                                                      >  1:378922/1‑140 (MQ=255)

                                             gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTg                                                                                           >  1:579480/1‑140 (MQ=255)

                                                cTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaa                                                                                        >  1:480820/1‑140 (MQ=255)

                                                   cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAt                                                                                     >  1:180393/1‑140 (MQ=255)

                                                           tACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCt                                                                             >  2:584639/1‑140 (MQ=255)

                                                             cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTgg                                                                           >  1:530250/1‑140 (MQ=255)

                                                                tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATa                                                                        >  2:295140/1‑140 (MQ=255)

                                                                  gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc                                                                      >  1:711084/1‑140 (MQ=255)

                                                                  gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc                                                                      >  1:501729/1‑140 (MQ=255)

                                                                  gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATAGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAACTTTAACGCTGGATAAc                                                                      >  2:192956/1‑140 (MQ=255)

                                                                          tCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCg                                                              <  2:734602/140‑1 (MQ=255)

                                                                            aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGa                                                            >  1:676826/1‑140 (MQ=255)

                                                                             gAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                           <  1:475778/140‑1 (MQ=255)

                                                                                aCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATgg                                                        >  2:687140/1‑140 (MQ=255)

                                                                                        ttctcACTAGAAAAACCGCAAAAAAGCAAAAAATACCGCGTTAAACCCACC‑CC‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTc                                                <  2:188589/139‑1 (MQ=255)

                                                                                         tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcc                                               >  2:80875/1‑140 (MQ=255)

                                                                                         tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcc                                               >  1:289125/1‑140 (MQ=255)

                                                                                             aCTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                           <  1:295140/140‑1 (MQ=255)

                                                                                              cTATTAAAACCGCTAAATAACAGAACATATCGCCGTAAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAACCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACTTTTCCCGGAATGGTTGAATTCCCCGcc                                          <  2:530250/140‑1 (MQ=255)

                                                                                               tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         <  2:480820/140‑1 (MQ=255)

                                                                                               tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         <  1:584639/140‑1 (MQ=255)

                                                                                               tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTAAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         <  2:711084/140‑1 (MQ=255)

                                                                                                  tAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑TCCC‑CCCCCCTCTCAGTGCAGTAAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      <  2:458527/140‑1 (MQ=255)

                                                                                                   aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         <  2:878002/136‑1 (MQ=255)

                                                                                                   aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         >  1:878002/1‑136 (MQ=255)

                                                                                                    aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                                    >  1:912888/1‑140 (MQ=255)

                                                                                                      aaCGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTTGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtat                                  >  1:848436/1‑140 (MQ=255)

                                                                                                       aCGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGGATGGTTGAATTCCCCGCCTCAGTtata                                 >  2:899779/1‑140 (MQ=255)

                                                                                                         gCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATg                               >  2:834611/1‑140 (MQ=255)

                                                                                                                   aGAACATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta                     <  1:646827/140‑1 (MQ=255)

                                                                                                                    gAACATATCGCCGTTAAGCCA‑TCCC‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTTGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGattat                    <  2:848436/140‑1 (MQ=255)

                                                                                                                       cATATCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTAc                 >  1:465544/1‑140 (MQ=255)

                                                                                                                        atatCGCCGTTAAGCCA‑TCCC‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACa                <  2:354334/140‑1 (MQ=255)

                                                                                                                          atCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACaaa              >  2:223787/1‑140 (MQ=255)

                                                                                                                          atCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACaaa              >  1:208844/1‑140 (MQ=255)

                                                                                                                          atCGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACaaa              >  2:465327/1‑140 (MQ=255)

                                                                                                                           tCGCCGTTAACCCA‑TCCC‑CCCCCCTCCCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCGGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAg             <  2:832144/140‑1 (MQ=255)

                                                                                                                            cGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAgg            >  1:609846/1‑140 (MQ=255)

                                                                                                                            cGCCGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAgg            >  1:832144/1‑140 (MQ=255)

                                                                                                                              ccGTTAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc          <  1:687140/140‑1 (MQ=255)

                                                                                                                                  tAAGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGt      >  1:584355/1‑140 (MQ=255)

                                                                                                                                   aaGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAgg            >  2:652210/1‑133 (MQ=255)

                                                                                                                                   aaGCCA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAgg            <  1:652210/133‑1 (MQ=255)

                                                                                                                                      ccA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGa  <  1:497402/140‑1 (MQ=255)

                                                                                                                                      ccA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGa  <  1:899779/140‑1 (MQ=255)

                                                                                                                                      ccA‑T‑CACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGa  <  2:180393/140‑1 (MQ=255)

AGAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCA‑T‑CA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGA  >  NC_000913/1712373‑1712645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `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