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 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,976,605	T→C	F110L (TTT→CTT)	wzxE →	O‑antigen translocase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,976,605	0	T	C	94.1%	111.3 / ‑1.9	34	F110L (TTT→CTT)	wzxE	O‑antigen translocase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (16/16); minor base G (1/1); total (17/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGTTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTTAT  >  NC_000913/3976470‑3976728

tACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTg                                                                                                                          >  2:474250/1‑139 (MQ=255)

    ttGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTaa                                                                                                                      >  2:971992/1‑139 (MQ=255)

     tGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGGTTGGTAAt                                                                                                                     >  2:797038/1‑139 (MQ=255)

                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAgggg                                                                                                      <  2:881619/137‑1 (MQ=255)

                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAgggg                                                                                                      >  1:881619/1‑137 (MQ=255)

                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCt                                                                                                    >  1:18956/1‑139 (MQ=255)

                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCT‑GTTTTTGTGCTGGCAGCTGCGCCAATCAACCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTg                                                                                                   >  1:542587/1‑139 (MQ=255)

                             aCAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATAc                                                                                                                   >  2:907077/1‑117 (MQ=255)

                             aCAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATAc                                                                                                                   <  1:907077/117‑1 (MQ=255)

                             aCAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGt                                                                                             >  2:179621/1‑139 (MQ=255)

                                   gcgcCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTg                                                                                       >  2:334966/1‑139 (MQ=255)

                                      ccgcGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATAcc                                                                                                                  <  1:397773/109‑1 (MQ=255)

                                      ccgcGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATAcc                                                                                                                  >  2:397773/1‑109 (MQ=255)

                                            ggTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGGTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                              <  1:797038/139‑1 (MQ=255)

                                            ggTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTa                                                                                                                       >  1:629312/1‑98 (MQ=255)

                                            ggTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTa                                                                                                                       <  2:629312/98‑1 (MQ=255)

                                                     ttCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATgggg                                                                     <  2:18956/139‑1 (MQ=255)

                                                      tcatcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGTGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGa                                                                    <  1:797469/139‑1 (MQ=255)

                                                        atcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTa                                                                                                                       <  2:32495/86‑1 (MQ=255)

                                                        atcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTa                                                                                                                       >  1:32495/1‑86 (MQ=255)

                                                                tGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTgggg                                                          <  1:179621/139‑1 (MQ=255)

                                                                 ggTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGc                                                         >  1:451134/1‑139 (MQ=255)

                                                                                tACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCaaa                                                                          <  2:222569/107‑1 (MQ=255)

                                                                                tACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCaaa                                                                          >  1:222569/1‑107 (MQ=255)

                                                                                       aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATgggg                                                                     <  2:424599/105‑1 (MQ=255)

                                                                                       aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATgggg                                                                     >  1:424599/1‑105 (MQ=255)

                                                                                        tGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGaa                                  <  1:11687/139‑1 (MQ=255)

                                                                                                   tttGTGCTGGCAGCTGCGCCAATCAACCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTcgcg                       <  2:542587/139‑1 (MQ=255)

                                                                                                          tGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGc                >  1:612713/1‑139 (MQ=255)

                                                                                                              aGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGt            <  2:804137/139‑1 (MQ=255)

                                                                                                                  gcgcCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATg        <  2:347707/139‑1 (MQ=255)

                                                                                                                    gcCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCg      <  1:971992/139‑1 (MQ=255)

                                                                                                                        aTCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTTAt  <  2:612713/139‑1 (MQ=255)

                                                                                                                        aTCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTTAt  >  1:157269/1‑139 (MQ=255)

TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGTTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTTAT  >  NC_000913/3976470‑3976728

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