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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,682,586	A→G	63.7%	Q439R (CAG→CGG)	ydgI →	predicted arginine/ornithine antiporter transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,682,586	0	A	G	63.7%	53.4 / 57.4	58	Q439R (CAG→CGG)	ydgI	predicted arginine/ornithine antiporter transporter
Reads supporting (aligned to +/- strand): ref base A (12/9); new base G (28/8); total (40/18)
Fisher's exact test for biased strand distribution p-value = 1.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCTGGTGGGATA  >  W3110S.gb/1682524‑1682652

ggggCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAAt                                                              <  1:3659612/69‑1 (MQ=255)

ggggCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAAt                                                              <  1:1806359/69‑1 (MQ=255)

ggggCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAAt                                                              <  1:2168527/69‑1 (MQ=255)

       ctgGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTg                                                       >  1:1787491/1‑69 (MQ=255)

                 tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                              <  1:616644/68‑1 (MQ=255)

                   tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGaa                                                                >  1:2857629/1‑48 (MQ=255)

                   tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGaa                                                                >  1:1103971/1‑48 (MQ=255)

                     cgcgcgCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:10068/1‑69 (MQ=255)

                     cgcgcgCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:583710/1‑69 (MQ=255)

                     cgcgcgCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGt                                          >  1:1871225/1‑68 (MQ=255)

                       cgcgcAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTa                                        <  1:1829597/68‑1 (MQ=255)

                       cgcgcAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTa                                        <  1:1141090/68‑1 (MQ=255)

                               aCGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATg                                              >  1:3320502/1‑54 (MQ=255)

                               aCGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCa                               >  1:203034/1‑69 (MQ=255)

                                cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAg                              >  1:1370173/1‑69 (MQ=255)

                                    tACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTcc                          <  1:2843289/69‑1 (MQ=255)

                                      cccATGTTAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:480194/1‑37 (MQ=38)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:3282159/1‑37 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:1962761/1‑37 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:1704549/1‑37 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:1158669/1‑37 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCt                                                        >  1:2278767/1‑37 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTTGCATGCTGTTAATTGCCTCAGTTcc                          >  1:3271998/1‑67 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:2056209/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:2282066/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:2340305/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:1752384/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:433817/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCg                         >  1:654102/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTAAGTTCCg                         >  1:1031000/1‑68 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        <  1:1461925/37‑1 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        <  1:2213813/37‑1 (MQ=255)

                                      cccATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        <  1:2264832/37‑1 (MQ=255)

                                       ccATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc                       >  1:3669513/1‑69 (MQ=255)

                                       ccATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc                       >  1:102605/1‑69 (MQ=255)

                                       ccATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc                       >  1:1090917/1‑69 (MQ=255)

                                        cATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTa                                        >  1:2433416/1‑51 (MQ=255)

                                        cATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        >  1:1624048/1‑35 (MQ=255)

                                        cATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        >  1:1514148/1‑35 (MQ=255)

                                        cATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                                        >  1:3544509/1‑35 (MQ=255)

                                        cATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc                       <  1:1856072/68‑1 (MQ=255)

                                        cATGATAATGTACTGAACCGTCAGGAAATGGAGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc                       <  1:1403067/68‑1 (MQ=255)

                                          tGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGAc                    >  1:507806/1‑69 (MQ=255)

                                          tGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGAc                    >  1:1789764/1‑69 (MQ=255)

                                            aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:2476078/1‑46 (MQ=255)

                                            aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:71385/1‑46 (MQ=255)

                                            aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:1339529/1‑46 (MQ=255)

                                            aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                         >  1:3690771/1‑46 (MQ=255)

                                            aTAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGAcc                   >  1:353489/1‑68 (MQ=255)

                                            aTAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGAcc                   >  1:2895822/1‑68 (MQ=255)

                                               aTGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                              <  1:2206168/38‑1 (MQ=255)

                                                tGTACTGAACCGTCTGGAAATGGTGCTGATTGGCATGCTGTTAATTGc                                   <  1:3495286/48‑1 (MQ=255)

                                                tGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGc                                   <  1:2632289/48‑1 (MQ=255)

                                                 gTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATg             >  1:3634670/1‑69 (MQ=255)

                                                 gTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATg             >  1:2806217/1‑69 (MQ=255)

                                                    cTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGc                                   <  1:1337105/44‑1 (MQ=255)

                                                           gTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCTGGTGGGAt   <  1:826682/69‑1 (MQ=255)

                                                             cAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCTGGTGGGATa  <  1:1118490/68‑1 (MQ=255)

                                                              aGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCtg          >  1:3520995/1‑59 (MQ=255)

                                                              aGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCtg          <  1:1414145/59‑1 (MQ=255)

                                                              aGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCtg          <  1:2903586/59‑1 (MQ=255)

                                                              aGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCtg          >  1:1912640/1‑59 (MQ=255)

                                                              aGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCtg          >  1:616611/1‑59 (MQ=255)

GGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCTGGTGGGATA  >  W3110S.gb/1682524‑1682652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A