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
A13 F1 I2 R1	92	50.6	2362856	94.3%	2228173	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,774,632	(A)_7→8	coding (1315/1704 nt)	yfjW →	CP4‑57 prophage, putative inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,774,625	1	.	A	100.0%	194.7 / NA	55	Y436* (TAT→TAA)	yfjW	CP4‑57 prophage, putative inner membrane protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (30/25); total (30/25)

CAAATATCGGATTTAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCG  >  NC_000913/2774488‑2774754

cAAATATCGGATTTAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCtat‑a                                                                                                                                  >  2:34851/1‑139 (MQ=255)

    tatCGGATTTAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaa                                                                                                                              >  1:451465/1‑139 (MQ=255)

    tatCGGATTTAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaa                                                                                                                              >  1:1177553/1‑139 (MQ=255)

           tttAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaaaaacata                                                                                                                       >  1:1147727/1‑134 (MQ=255)

                                 aaTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAatatat                                                                                                  >  2:1053998/1‑139 (MQ=255)

                                  aTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCt                                                                                                               >  1:510338/1‑125 (MQ=255)

                                  aTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCt                                                                                                               <  2:510338/125‑1 (MQ=255)

                                  aTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 <  1:1053998/139‑1 (MQ=255)

                                  aTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 <  2:810470/139‑1 (MQ=255)

                                  aTGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 >  1:807941/1‑139 (MQ=255)

                                    gCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatgat                                                                                               <  2:47351/139‑1 (MQ=255)

                                        aTTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaaaaaca                                                                                                                         >  2:259694/1‑105 (MQ=255)

                                        aTTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaaaaaca                                                                                                                         <  1:259694/108‑4 (MQ=255)

                                             ttAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGc                                                                                      >  2:864620/1‑139 (MQ=255)

                                                       ttttACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAAt                                                                            <  2:807941/139‑1 (MQ=255)

                                                       ttttACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAAt                                                                            >  1:1103360/1‑139 (MQ=255)

                                                               gTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatgat                                                                                               <  2:556948/112‑1 (MQ=255)

                                                               gTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatgat                                                                                               >  1:556948/1‑112 (MQ=255)

                                                               gTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCa                                                                    <  2:1147727/139‑1 (MQ=255)

                                                                  cTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTg                                                                 <  1:34851/139‑1 (MQ=255)

                                                                    aaaaCCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTgag                                                               <  2:1177553/139‑1 (MQ=255)

                                                                    aaaaCCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTgag                                                               <  2:451465/139‑1 (MQ=255)

                                                                          aGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAAc                                                         >  1:1160372/1‑139 (MQ=255)

                                                                          aGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAAc                                                         >  1:1101118/1‑139 (MQ=255)

                                                                           gatgatATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCa                                                                    <  1:235192/127‑1 (MQ=255)

                                                                           gatgatATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCa                                                                    >  2:235192/1‑127 (MQ=255)

                                                                           gatgatATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACa                                                        >  2:740643/1‑139 (MQ=255)

                                                                                 attattAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAg                                                                                       >  1:432032/1‑102 (MQ=255)

                                                                                 attattAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAg                                                                                       <  2:432032/102‑1 (MQ=255)

                                                                                   tattaATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAat                                                                                                      >  1:277742/1‑85 (MQ=255)

                                                                                   tattaATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAat                                                                                                      <  2:277742/85‑1 (MQ=255)

                                                                                          taCAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGttt                                         >  2:22681/1‑139 (MQ=255)

                                                                                          taCAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATACATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGttt                                         >  2:556870/1‑139 (MQ=255)

                                                                                            caacaaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAg                                       >  1:367307/1‑139 (MQ=255)

                                                                                               caaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATACATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTAt                                    <  1:556870/139‑1 (MQ=255)

                                                                                                    gCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaaaaa                                                                                                                           <  1:723371/46‑2 (MQ=255)

                                                                                                    gCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑aaaaaaaa                                                                                                                           >  2:723371/1‑45 (MQ=255)

                                                                                                        ttCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGaa                           <  1:740643/139‑1 (MQ=255)

                                                                                                             tactacTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTgag                                                               <  2:668551/98‑1 (MQ=255)

                                                                                                             tactacTCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTgag                                                               >  1:668551/1‑98 (MQ=255)

                                                                                                                tactCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGt                   >  1:287803/1‑139 (MQ=255)

                                                                                                                  ctaaaGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGc                                                            <  2:653859/93‑1 (MQ=255)

                                                                                                                  ctCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 <  1:1037066/59‑1 (MQ=255)

                                                                                                                  ctCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 >  2:1037066/1‑59 (MQ=255)

                                                                                                                  ctCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCg                 >  2:163524/1‑139 (MQ=255)

                                                                                                                  ctCAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCg                 >  2:157710/1‑139 (MQ=255)

                                                                                                                  ctCAAGACTGATTTTGCGATCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGc                                                            >  1:653859/1‑96 (MQ=255)

                                                                                                                    cAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGtt               <  2:367307/139‑1 (MQ=255)

                                                                                                                    cAAGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGtt               <  1:476653/139‑1 (MQ=255)

                                                                                                                     aaGACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTa              >  1:1015007/1‑139 (MQ=255)

                                                                                                                     aaGACTGATTTTGCGTTCTATAAAAAAAACATACAAGAAGCTTGTTAAAATATATGATGAATTAAGCAATGGAAAATTATCTTCACTGAGAGCAAAAGGTATCTCCCAGTTTAGAATAAACGGGAAACATTTGTCGTTa              >  2:468490/1‑139 (MQ=255)

                                                                                                                       gACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 <  2:1133457/54‑1 (MQ=255)

                                                                                                                       gACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 >  1:1133457/1‑54 (MQ=255)

                                                                                                                       gACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAg            <  1:659533/139‑1 (MQ=255)

                                                                                                                       gACTGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAg            >  1:14614/1‑139 (MQ=255)

                                                                                                                          tGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATc                                   <  1:518970/113‑1 (MQ=255)

                                                                                                                          tGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATc                                   >  2:518970/1‑113 (MQ=255)

                                                                                                                          tGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGcc         >  2:88999/1‑139 (MQ=255)

                                                                                                                          tGATTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGcc         >  1:313958/1‑139 (MQ=255)

                                                                                                                            aTTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 >  1:885326/1‑49 (MQ=255)

                                                                                                                            aTTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATatg                                                                                                 <  2:885326/49‑1 (MQ=255)

                                                                                                                            aTTTTGCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAg       >  2:1047097/1‑139 (MQ=255)

                                                                                                                                 gCGTTCTATAAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCg  <  1:163524/139‑1 (MQ=255)

CAAATATCGGATTTAACAAATACGTATAACATTAATGCAAATTACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCG  >  NC_000913/2774488‑2774754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A