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
A4 F28 I1 R1	159	82.1	2830106	99.3%	2810295	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,002,039	T→C	intergenic (‑250/+71)	fliA ← / ← fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,002,039	0	T	C	97.8%	164.1 / ‑4.2	46	intergenic (‑250/+71)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/26); total (19/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAACACGGAGTT  >  NC_000913/2001904‑2002172

ccAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGc                                                                                                                                   <  2:562855/140‑1 (MQ=255)

 cAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGcc                                                                                                                                  >  1:1311916/1‑140 (MQ=255)

   ggCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTg                                                                                                                                >  1:348952/1‑140 (MQ=255)

            aaaCCCCGCCGGTGGCAGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAagcgca                                                                                                                       <  2:1267952/140‑1 (MQ=255)

                  cgccgGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCAt                                                                                                                 >  1:687888/1‑140 (MQ=255)

                      ggTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAgg                                                                                                             <  1:1364393/140‑1 (MQ=255)

                       gTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGc                                                                                                            >  1:918817/1‑140 (MQ=255)

                         ggCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCaa                                                                                                          >  1:901302/1‑140 (MQ=255)

                                 aGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGt                                                                                                  <  2:468996/140‑1 (MQ=255)

                                 aGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCCTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGt                                                                                                  <  1:692422/140‑1 (MQ=255)

                                     cGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGcc                                                                                              <  1:1294333/140‑1 (MQ=255)

                                      gTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCg                                                                                             <  2:686248/140‑1 (MQ=255)

                                       ttGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGt                                                                                            <  2:707391/140‑1 (MQ=255)

                                       ttGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGt                                                                                            <  1:1170628/140‑1 (MQ=255)

                                           tGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGt                                                                                        <  1:299450/140‑1 (MQ=255)

                                              cAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGtctc                                                                                     <  2:96281/140‑1 (MQ=255)

                                                    gcgcTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTaa                                                                               <  2:97480/140‑1 (MQ=255)

                                                     cgcTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAAt                                                                              <  1:6856/140‑1 (MQ=255)

                                                              ttGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTACAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACa                                                                     <  1:923066/140‑1 (MQ=255)

                                                                  cGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGa                                                                 >  1:192339/1‑140 (MQ=255)

                                                                   ggATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGAt                                                                <  1:1237145/140‑1 (MQ=255)

                                                                      tGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTaa                                                             <  2:821944/140‑1 (MQ=255)

                                                                          gcgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCt                                                         <  1:9212/140‑1 (MQ=255)

                                                                           cgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTg                                                        >  2:659637/1‑140 (MQ=255)

                                                                            gTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgc                                                       <  1:829711/140‑1 (MQ=255)

                                                                                aCGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgcagca                                                   <  2:1311916/140‑1 (MQ=255)

                                                                                aCGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgcagca                                                   <  2:560246/140‑1 (MQ=255)

                                                                                    cTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAgaga                                               >  1:1303867/1‑140 (MQ=255)

                                                                                    cTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAgaga                                               >  2:1082798/1‑140 (MQ=255)

                                                                                     ttATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGAc                                              >  1:1156981/1‑140 (MQ=255)

                                                                                            gCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACct                                       >  2:561432/1‑140 (MQ=255)

                                                                                            gCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACct                                       >  1:920460/1‑140 (MQ=255)

                                                                                                aCAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACctgctg                                   >  2:60118/1‑140 (MQ=255)

                                                                                                aCAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACctgctg                                   <  2:775719/140‑1 (MQ=255)

                                                                                                 cAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCtgctgc                                  >  1:875814/1‑140 (MQ=255)

                                                                                                           cAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCtgctgc                                  <  2:357140/130‑1 (MQ=255)

                                                                                                           cAAATTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCtgctgc                                  >  1:357140/1‑130 (MQ=255)

                                                                                                            aaaTTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGtt                       >  2:491735/1‑140 (MQ=255)

                                                                                                            aaaTTCAATAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGtt                       >  1:1412338/1‑140 (MQ=255)

                                                                                                                   aTAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCtttt                >  1:92415/1‑140 (MQ=255)

                                                                                                                    tAAATTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTg               <  2:920460/140‑1 (MQ=255)

                                                                                                                      aaTTGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGcc             <  2:1326429/140‑1 (MQ=255)

                                                                                                                         tGCAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAac          <  1:60118/140‑1 (MQ=255)

                                                                                                                           cAATTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAacac        <  2:901302/140‑1 (MQ=255)

                                                                                                                            aaTTCAACTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAACACg       <  1:751250/140‑1 (MQ=255)

                                                                                                                                 aaCTTGCAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAACACGGAGtt  >  1:670917/1‑140 (MQ=255)

CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGACAGAACCTGCTGCGGTACCTGGTTAGCTTTTGCCAACACGGAGTT  >  NC_000913/2001904‑2002172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A