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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,286,523	A→G	47.9%	F288F (TTT→TTC)	argC ←	N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,286,523	0	A	G	47.9%	‑1.6 / 63.0	71	F288F (TTT→TTC)	argC	N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
Reads supporting (aligned to +/- strand): ref base A (13/24); new base G (20/14); total (33/38)
Fisher's exact test for biased strand distribution p-value = 5.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

GTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCA  >  minE/2286459‑2286568

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGTCAAAACCGATATCGCAGAAt                                            <  1:3064846/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:88058/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:2025188/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:2069389/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:3372/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:515043/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:1473641/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:221661/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:3250148/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:3234566/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:2994048/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:2581753/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:2860365/68‑1 (MQ=255)

gTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAAt                                            <  1:1099173/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:2594120/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:2988079/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:2706713/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:1957426/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:411768/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:162422/68‑1 (MQ=255)

     ttGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAg                                       <  1:138080/68‑1 (MQ=255)

      tGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGc                                      >  1:797343/1‑68 (MQ=255)

                    acaATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCa                                        >  1:62307/1‑52 (MQ=255)

                    acaATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTc                       <  1:1140733/69‑1 (MQ=255)

                    acaATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTc                       >  1:656735/1‑69 (MQ=255)

                     caATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTc                       <  1:3405311/68‑1 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAgc                    >  1:861270/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:642836/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:271/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:875973/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:697619/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:3157968/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:3427953/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:408951/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:405078/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:1133013/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:2638402/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:1645774/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:1943795/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:1190034/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:1586983/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:2166704/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:2209457/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:2285931/1‑69 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAg                     >  1:1182129/1‑68 (MQ=255)

                       ataatCAGATGCTCGCCCTGAACGGCAAAACCGATATCGCAGAATCGCAGTCCAACGACATTTTTCAgc                    >  1:3111834/1‑69 (MQ=255)

                       ataatCAGATGCTAGCCCTGAACGGCAAAACCGATATCGCAGAATGGCAGTCCAACGACATTTTTCAgc                    >  1:3258147/1‑69 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:2270271/69‑1 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:509765/69‑1 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:2344992/69‑1 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:724412/69‑1 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:2884444/69‑1 (MQ=255)

                            cAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCgg               <  1:1678027/69‑1 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCGCAACGACATTTTTCAGCGCCgg               <  1:1060702/57‑1 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACa                             >  1:2862558/1‑43 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:461517/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:1000464/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:1126107/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:299323/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:1294148/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:578538/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:2263016/1‑68 (MQ=255)

                                        cTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGt    >  1:1693389/1‑68 (MQ=255)

                                         tGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:683017/69‑1 (MQ=255)

                                         tGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:2401053/69‑1 (MQ=255)

                                                    cccGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:1271912/58‑1 (MQ=255)

                                                    cccGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:1258048/58‑1 (MQ=255)

                                                    cccGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:705294/58‑1 (MQ=255)

                                                    cccGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:2605288/58‑1 (MQ=255)

                                                    cccGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:281012/58‑1 (MQ=255)

                                                       gATATCGCAAAATGGCAGCACAACGACATTTTTCAGCGCCGGAACGCCTTTGTCa  <  1:712846/55‑1 (MQ=255)

GTAAGTTGTCTTCGGTCGCCACAATAATCAGATGCTCGCCCTGAACGGCAAACCCGATATCGCAAAATGGCAGCCCAACGACATTTTTCAGCGCCGGAACGCCTTTGTCA  >  minE/2286459‑2286568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A