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
A11 F1 I1 R1	757	76.1	3598070	93.4%	3360597	108.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,354,288	G→A	F77F (TTC→TTT)	sapC ←	antimicrobial peptide transport ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,354,288	0	G	A	100.0%	115.9 / NA	37	F77F (TTC→TTT)	sapC	antimicrobial peptide transport ABC transporter permease
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/18); total (19/18)

GGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGGAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATACACAGTACAGCCAGCCCCGCGCAGCCGTACAGG  >  NC_000913/1354179‑1354423

ggCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAgc                                                                                                                   <  2:996589/132‑1 (MQ=255)

ggCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAgc                                                                                                                   >  1:996589/1‑132 (MQ=255)

ggCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCa                                                                                                            >  1:266965/1‑139 (MQ=255)

   cacaGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGa                                                                                                         >  1:336801/1‑139 (MQ=255)

     caGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAgaaagaaa                                                                                                                                   >  2:296296/1‑111 (MQ=255)

     caGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAgaaagaaa                                                                                                                                   <  1:296296/111‑1 (MQ=255)

     caGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGAcg                                                                                                       >  2:985625/1‑139 (MQ=255)

            tcgCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCaa                                                                                                <  1:985625/139‑1 (MQ=255)

            tcgCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCaa                                                                                                <  1:306668/139‑1 (MQ=255)

            tcgCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCaa                                                                                                <  1:1189982/139‑1 (MQ=255)

                      cGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGAcggc                                                                                                     >  2:918964/1‑124 (MQ=255)

                      cGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGAcggc                                                                                                     <  1:918964/124‑1 (MQ=255)

                      cGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATaa                                                                                      <  2:266965/139‑1 (MQ=255)

                                      ccacccacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGt                                                                      >  1:109560/1‑139 (MQ=255)

                                         cccacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGa                                                                   <  1:879070/139‑1 (MQ=255)

                                                  ggCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGt                                                                      <  1:303532/127‑1 (MQ=255)

                                                  ggCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGt                                                                      >  2:303532/1‑127 (MQ=255)

                                                   gcgcAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAgc                                                                                                                   >  1:1343881/1‑81 (MQ=255)

                                                   gcgcAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAgc                                                                                                                   <  2:1343881/81‑1 (MQ=255)

                                                   gcgcAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAg                                                          <  1:1078888/138‑1 (MQ=255)

                                                   gcgcAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAg                                                          >  2:1078888/1‑138 (MQ=255)

                                                   gcgcAGCTCCGCTCAGTAAACGACTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAgg                                                         >  1:374196/1‑139 (MQ=255)

                                                    cgcAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGgc                                                        >  2:363122/1‑139 (MQ=255)

                                                         cTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCaaa                                                   >  1:712177/1‑139 (MQ=255)

                                                            cGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGt                                                                      >  1:1745098/1‑117 (MQ=255)

                                                            cGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGt                                                                      <  2:1745098/117‑1 (MQ=255)

                                                              cTCAGTAAGCGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAACCCAgc                                              >  1:1299453/1‑139 (MQ=255)

                                                              cTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAAc                                                                                     <  2:1268694/100‑1 (MQ=255)

                                                              cTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCAAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAAc                                                                                     >  1:1268694/1‑100 (MQ=255)

                                                                          cTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATac                                  <  2:374196/139‑1 (MQ=255)

                                                                               aaCATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCaa                                                                                                >  1:686622/1‑72 (MQ=255)

                                                                               aaCATCGCGTCCGAGGTCGTCAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCaa                                                                                                <  2:686622/72‑1 (MQ=255)

                                                                                              gtcgtcAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATACACAGTACAGCCAGCCCcgcg              >  2:573482/1‑139 (MQ=255)

                                                                                                cgtcAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATACACAGTACAGCCAGCCCCGCGCa            <  2:109560/139‑1 (MQ=255)

                                                                                                   cAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCg                                                                    <  2:886602/80‑1 (MQ=255)

                                                                                                   cAGTCCCCAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCg                                                                    >  1:886602/1‑80 (MQ=255)

                                                                                                        cccAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAgg                                                         >  2:1535574/1‑86 (MQ=255)

                                                                                                        cccAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAgg                                                         <  1:1535574/86‑1 (MQ=255)

                                                                                                          cAGAAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATACACAGTACAGCCAGCCCCGCGCAGCCGTACAgg  <  2:336801/139‑1 (MQ=255)

GGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGGAAGAAAGAAACTTCGCCATAGCGCGACCATGACGGCGGCAATAATTGATAACCGAGAAATTGCTGGTCGATGCCGTAAGGCGCAAACCAGCCGCCAAAAATACACAGTACAGCCAGCCCCGCGCAGCCGTACAGG  >  NC_000913/1354179‑1354423

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A