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 F224 I0 R1	1457	284.0	9290224	95.7%	8890744	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,205,954	G→T	34.1%	L51F (TTG→TTT)	mcrA →	putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,205,954	0	G	T	34.1%	68.4 / 34.3	41	L51F (TTG→TTT)	mcrA	putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene
Reads supporting (aligned to +/- strand): ref base G (11/16); new base T (4/10); total (15/26)
Fisher's exact test for biased strand distribution p-value = 5.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAATAATGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACGCTTGAAGA  >  CP009273/1205815‑1206099

ataataATGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTg                                                                                                                                         >  1:3887853/1‑150 (MQ=255)

ataataATGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTg                                                                                                                                         >  1:3887781/1‑150 (MQ=255)

ataataATGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTg                                                                                                                                         >  1:3887780/1‑150 (MQ=255)

  aataatGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGAGGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTGgt                                                                                                                                       >  2:2931095/1‑150 (MQ=255)

            ttGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAg                                                                                                                             <  1:2647494/150‑1 (MQ=255)

             tGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGt                                                                                                                            >  1:2388545/1‑150 (MQ=255)

             tGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGt                                                                                                                            >  1:2388556/1‑150 (MQ=255)

             tGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGt                                                                                                                            >  1:2388631/1‑150 (MQ=255)

                aCTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCgt                                                                                                                         >  1:302444/1‑150 (MQ=255)

                     aaGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGtat                                                                                                                    >  1:1831500/1‑150 (MQ=255)

                     aaGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGtat                                                                                                                    >  1:1831544/1‑150 (MQ=255)

                      aGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGtata                                                                                                                   <  2:4352550/150‑1 (MQ=255)

                        cTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATc                                                                                                                 <  1:1560817/150‑1 (MQ=255)

                               ttCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGCTTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGtc                                                                                                          <  1:3120605/150‑1 (MQ=255)

                               ttCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGtc                                                                                                          <  1:3119872/150‑1 (MQ=255)

                               ttCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGtc                                                                                                          <  1:3119893/150‑1 (MQ=255)

                                     aGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGtcatcatc                                                                                                    <  1:1042163/150‑1 (MQ=255)

                                                 tGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACa                                                                                        <  1:1884546/150‑1 (MQ=255)

                                                 tGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACa                                                                                        <  1:1663069/150‑1 (MQ=255)

                                                  ggTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACat                                                                                       <  2:1306479/150‑1 (MQ=255)

                                                                                 ggCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAACACATATGCATTCTTTGGATGAAAGAAAAatccatc                                                        <  2:302444/150‑1 (MQ=255)

                                                                                     gggTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTgg                                                    >  2:3387327/1‑150 (MQ=255)

                                                                                          aCAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAat                                               <  2:75016/150‑1 (MQ=255)

                                                                                            aGAAACAAAGATGACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAatat                                             >  1:2766296/1‑150 (MQ=255)

                                                                                                   aaGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACtt                                      >  2:2960552/1‑150 (MQ=255)

                                                                                                             tatCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAACACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTaa                            <  1:769301/150‑1 (MQ=255)

                                                                                                             tatCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAACACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTaa                            <  1:769287/150‑1 (MQ=255)

                                                                                                                 gCTCTTGATTATATCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGc                        <  1:81414/150‑1 (MQ=255)

                                                                                                                 gCTCTTGATTATATCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGc                        <  1:81415/150‑1 (MQ=255)

                                                                                                                     ttGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGccccc                    <  1:660035/150‑1 (MQ=255)

                                                                                                                     ttGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGccccc                    <  1:471419/150‑1 (MQ=255)

                                                                                                                     ttGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGccccc                    <  1:471186/150‑1 (MQ=255)

                                                                                                                     ttGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGccccc                    <  1:471174/150‑1 (MQ=255)

                                                                                                                       gATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCcgc                  >  1:3746489/1‑150 (MQ=255)

                                                                                                                          tataTCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGat               <  2:3887780/150‑1 (MQ=255)

                                                                                                                          tataTCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGat               <  2:3887781/150‑1 (MQ=255)

                                                                                                                          tataTCATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGat               <  2:3887853/150‑1 (MQ=255)

                                                                                                                               cATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACg          <  1:1719521/150‑1 (MQ=255)

                                                                                                                               cATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACg          <  1:1719589/150‑1 (MQ=255)

                                                                                                                               cATTGAACGGTTTGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACg          <  1:1719636/150‑1 (MQ=255)

                                                                                                                                aTTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAACACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACGc         >  1:2968348/1‑150 (MQ=255)

                                                                                                                                       ggttggttGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACGCTTGAAGa  <  2:1831500/150‑1 (MQ=255)

                                                                                                                                       ggttggttGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACGCTTGAAGa  <  2:1831544/150‑1 (MQ=255)

ATAATAATGGAATTGAACTGAAAGCTGAGTGTTCGATAGGTGAAGAGGATGGTGTTTATGGTCTAATCCTTGAGTCGTGGGGGCCGGGTGACAGAAACAAAGATTACAATATCGCTCTTGATTATATCATTGAACGGTTGGTTGATTCTGGTGTATCCCAAGTCGTAGTATATCTGGCGTCATCATCAGTCAGAAAACATATGCATTCTTTGGATGAAAGAAAAATCCATCCTGGTGAATATTTTACTTTGATTGGTAATAGCCCCCGCGATATACGCTTGAAGA  >  CP009273/1205815‑1206099

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A