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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,561,890	G→A	R89H (CGC→CAC)	yffN →	CPZ‑55 prophage; uncharacterized protein YffN

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,561,890	0	G	A	100.0%	150.3 / NA	43	R89H (CGC→CAC)	yffN	CPZ‑55 prophage; uncharacterized protein YffN
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/21); total (22/21)

CGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCGCGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAA  >  NC_000913/2561757‑2562023

cGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTc                                                                                                                                   >  2:614697/1‑138 (MQ=255)

cGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTc                                                                                                                                   <  1:614697/138‑1 (MQ=255)

cGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCAt                                                                                                                                 >  1:397397/1‑140 (MQ=255)

cGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCAt                                                                                                                                 >  1:576975/1‑140 (MQ=255)

cGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCAt                                                                                                                                 >  2:556415/1‑140 (MQ=255)

  tGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGc                                                                                                                               >  2:235701/1‑140 (MQ=255)

  tGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGc                                                                                                                               >  2:736284/1‑140 (MQ=255)

    ggTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGt                                                                                                                             >  1:196334/1‑140 (MQ=255)

    ggTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGt                                                                                                                             >  2:594574/1‑140 (MQ=255)

        tgtTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAAc                                                                                                                         >  2:466654/1‑140 (MQ=255)

        tgtTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAAc                                                                                                                         <  1:736284/140‑1 (MQ=255)

        tgtTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAAc                                                                                                                         <  2:576975/140‑1 (MQ=255)

           tGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAg                                                                                                                      <  2:546757/140‑1 (MQ=255)

            gAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGa                                                                                                                     <  2:200747/140‑1 (MQ=255)

                 tGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGACCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTc                                                                                                                >  2:786787/1‑140 (MQ=255)

                     cAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATg                                                                                                            <  1:594574/140‑1 (MQ=255)

                       gCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGcc                                                                                                          <  1:525225/140‑1 (MQ=255)

                            gtggATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATGAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGaa                                                                                                     >  2:702598/1‑140 (MQ=255)

                             tggATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGaaa                                                                                                    >  2:765966/1‑140 (MQ=255)

                                      tGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACg                                                                                           >  2:519978/1‑140 (MQ=255)

                                        aGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGaa                                                                                         <  1:519978/140‑1 (MQ=255)

                                          cTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAAt                                                                                       <  1:84850/140‑1 (MQ=255)

                                                cAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAg                                                                                 <  2:196334/140‑1 (MQ=255)

                                                        tGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTa                                                                         <  2:645031/140‑1 (MQ=255)

                                                             ccGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATa                                                                                   <  2:352275/125‑1 (MQ=255)

                                                             ccGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATa                                                                                   >  1:649382/1‑125 (MQ=255)

                                                             ccGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATa                                                                                   >  1:352275/1‑125 (MQ=255)

                                                             ccGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATa                                                                                   <  2:649382/125‑1 (MQ=255)

                                                               ggAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGAttt                                                                  >  1:532908/1‑140 (MQ=255)

                                                                      aTGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAgcg                                                           >  1:595163/1‑140 (MQ=255)

                                                                              gagCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGa                                                   <  1:765966/140‑1 (MQ=255)

                                                                                gCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACg                                                 <  1:235701/140‑1 (MQ=255)

                                                                                gCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACg                                                 <  1:556415/140‑1 (MQ=255)

                                                                                    cTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTcc                                             >  2:13824/1‑140 (MQ=255)

                                                                                    cTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTcc                                             >  2:376021/1‑140 (MQ=255)

                                                                                              gaatcgaatcAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGc                                   >  1:345795/1‑140 (MQ=255)

                                                                                               aatcgaatcAAGGAAGGTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCt                                  <  2:345795/140‑1 (MQ=255)

                                                                                                             aggTGGCAATTGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAg                    <  2:532908/140‑1 (MQ=255)

                                                                                                                      ttGCTGCCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAAtt           >  1:664694/1‑140 (MQ=255)

                                                                                                                       tgctgcCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTa          <  1:376021/140‑1 (MQ=255)

                                                                                                                       tgctgcCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTa          <  2:595163/140‑1 (MQ=255)

                                                                                                                         ctgcCCTGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAAt        >  1:201859/1‑140 (MQ=255)

                                                                                                                               tGCTTCACGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTaa  <  2:664694/140‑1 (MQ=255)

CGTGGGTGTGTTGAGCTTGTCCAGCCTGGTGGATTCGATGAGCTGGTTCAGATCTATGAGGCCGGAGGCGATGGAATAGAGCCACTCAATTGTGGAATCGAATCAAGGAAGGTGGCAATTGCTGCCCTGCTTCGCGTCATGCGTGAACCAGACTTTCAATGCCTGGAAATGGTTCACGAAATCATAAGAATTGCTAGAGATTTGGAAGCGCCAGTTGACGCTCCGTTAGATTGCTAACGCCAAAATTAGCGCTGAATTAATGGGTAA  >  NC_000913/2561757‑2562023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A