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
A1 F113 I2 R1	11	53.1	1830242	95.2%	1742390	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,020,961	A→G	intergenic (‑42/‑177)	sulA ← / → sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,020,961	0	A	G	97.8%	135.8 / ‑4.1	46	intergenic (‑42/‑177)	sulA/sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (30/14); total (30/16)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.79e-01

AGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGT  >  NC_000913/1020825‑1021099

aGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTCTGGAGGTACAGTGCATCCa                                                                                                                                      >  2:121632/1‑143 (MQ=255)

 gCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTCTCGATGTACACTGCATCCAg                                                                                                                                     >  2:87066/1‑143 (MQ=255)

 gCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAg                                                                                                                                     >  2:60546/1‑143 (MQ=255)

         gTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGTACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGCACTGTACATCCatacagtaac                                                                                                                             <  1:229060/143‑10 (MQ=255)

          tAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCTAGGCCCCGTGAGGTACTGTATGGATGTACAGTGCATACAGTGAccacaa                                                                                                                            >  2:417869/1‑143 (MQ=255)

           aGTGTGTTGCGTAGAGGCACGAGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGGTGTGCATAGCCTGAAGTGTACATAATCACGCCAGCCCATGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACaaa                                                                                                                           <  1:122513/143‑1 (MQ=255)

            gtgtTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAg                                                                                                                          >  2:350059/1‑143 (MQ=255)

             tgtTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCCGTGGCAACAAAGa                                                                                                                         >  2:270611/1‑143 (MQ=255)

              gtcttCCGTAGAGACACGCGCAATTTTACCTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGAt                                                                                                                        <  2:708618/140‑1 (MQ=255)

               ttttCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATc                                                                                                                       >  1:715849/1‑143 (MQ=255)

                     gTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGGGAACGACACCATGGATGTACAGTGCATCCTGTGACAACAAAAATCAACCCt                                                                                                                 >  2:622403/1‑143 (MQ=255)

                           agacGCGCAATGTTGCTGGCTGCGGAAGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTc                                                                                                           <  2:26369/141‑1 (MQ=255)

                                    aTTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTACGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGc                                                                                                  <  2:477191/143‑1 (MQ=255)

                                       ttACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGCCAACAAGGAGCAACCCTATTTTCGGAAAGAGCCTc                                                                                               >  2:30266/1‑143 (MQ=255)

                                       ttACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATACAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTc                                                                                               >  2:463881/1‑143 (MQ=255)

                                              ctgcGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAAtt                                                                                        <  2:681481/143‑1 (MQ=255)

                                                         aaCGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCGGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGt                                                                             >  2:873823/1‑143 (MQ=255)

                                                               gaagaaCGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACggg                                                                       <  2:883125/143‑1 (MQ=255)

                                                               gaagaaCGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTAGTTTCGGAAAGAGCCTCGCAAGTTTTGTCGTGGGTGACggg                                                                       >  2:281463/1‑143 (MQ=255)

                                                                      gATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACAt                                                                <  1:720332/143‑1 (MQ=255)

                                                                       aTGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAGAACATa                                                               >  1:819823/1‑143 (MQ=255)

                                                                               aGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGAGACGGGAAAACATAAATTAATc                                                       >  1:767503/1‑143 (MQ=255)

                                                                                   tGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGc                                                   >  1:83783/1‑143 (MQ=255)

                                                                                   tGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGc                                                   >  1:502371/1‑143 (MQ=255)

                                                                                    gAAATGAACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAATGAATACAGTGACAACAAAGATCAACCCTAATTTCGGAAAAAGCCTCGCAAAATACATCGTTGGTGACGGGAAAAAATaaactcaactagcc                                                  >  1:817794/1‑132 (MQ=255)

                                                                                          tACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTAGCCCCTTaa                                            >  1:562517/1‑143 (MQ=255)

                                                                                           aCATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAg                                           >  1:400130/1‑143 (MQ=255)

                                                                                               aatcaatcCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCttgaccaga                                       >  2:415382/1‑136 (MQ=255)

                                                                                                atcaatcCAGCCCCTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGTAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATaa                                      <  2:315180/143‑1 (MQ=255)

                                                                                                atcaatcCAGCCCCTGTGAGTGACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATaa                                      <  2:790960/143‑1 (MQ=255)

                                                                                                          ccccTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCATAtt                            >  2:95463/1‑143 (MQ=255)

                                                                                                             cTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAACACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTc                         <  2:626290/143‑1 (MQ=255)

                                                                                                             cTGTGAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGGTGCCGATTTTc                         >  2:611187/1‑143 (MQ=255)

                                                                                                                tgAGTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTa                      <  1:237007/143‑1 (MQ=255)

                                                                                                                  tggtagggTATGGATGTACAGTGCATCCGGTGACAACAAAGTTCCACCCTATTTTCGGAAAGAGCCTCGCGAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGt                    <  1:635194/136‑1 (MQ=255)

                                                                                                                   gTTACTGTATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGtt                   <  2:852815/143‑1 (MQ=255)

                                                                                                                          tATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGAt            >  2:611395/1‑143 (MQ=255)

                                                                                                                          tATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGATGGTGGCGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGAt            >  1:245613/1‑143 (MQ=255)

                                                                                                                          tATGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATCTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTCGTTAACGGAt            >  1:414524/1‑143 (MQ=255)

                                                                                                                          tATGGATGTACAGTGCATCCAGTGACAACAAAAATCAACCCTATGTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTACGAATAAGTTGCCTGTTGTCGTAGTTAACGGAt            >  2:361598/1‑143 (MQ=255)

                                                                                                                           aTGGATTTACAGGGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATc           <  1:525777/143‑1 (MQ=255)

                                                                                                                            tGGATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATcc          >  2:804546/1‑143 (MQ=255)

                                                                                                                            tGGATGTAATGTTCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATcc          <  2:478410/143‑1 (MQ=255)

                                                                                                                             ggATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAACTTAATCTTGCCCCTTACGAATATGTTGCTTATTGTCGTAGTTAACGGGTCCg         >  2:7231/1‑143 (MQ=255)

                                                                                                                             ggATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCg         >  1:265955/1‑143 (MQ=255)

                                                                                                                              gATGTACAGTGCATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATGTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGt        >  2:447990/1‑143 (MQ=255)

                                                                                                                                  tacagtgcaTCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAAt    <  2:51723/143‑1 (MQ=255)

                                                                                                                                   acagtgcaTCCAGTGACAACAAAGATCAACCCGATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCGTCAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAGtg   >  1:477825/1‑143 (MQ=255)

                                                                                                                                    cagtgcaTCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAAtgt  <  2:400130/143‑1 (MQ=255)

                                                                                                                                    cagtgcaTCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATGTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAAtgt  <  1:817972/143‑1 (MQ=255)

AGCCCGGCTGTAGTGTTTTCCGTAGAGACACGCGCAATTTTACTTGCTGCGGATGAGAACGACGAAGAACGATGTGCATAGCCTGAAGTGTACATAATCAATCCAGCCCCTGTGAGTTACTGTATGGATGTACAGTACATCCAGTGACAACAAAGATCAACCCTATTTTCGGAAAGAGCCTCGCAAATTTTGTCGTTGGTGACGGGAAAACATAAATTAATCTTGCCCCTTAAGAATAAGTTGCCTATTTTCGTAGTTAACGGATCCGTTAATGT  >  NC_000913/1020825‑1021099

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A