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 F191 I1 R2	32	34.5	741600	95.9%	711194	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,502,141	C→A	A222D (GCC→GAC)	USA300HOU_2364 →	AraC transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,502,141	0	C	A	97.1%	104.6 / NA	35	A222D (GCC→GAC)	USA300HOU_2364	AraC transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (18/16); minor base T (1/0); total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAATCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCA  >  CP000730/2502004‑2502274

tGAATCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACgg                                                                                                                                    <  2:267170/141‑1 (MQ=255)

tGAATCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACgg                                                                                                                                    >  1:282041/1‑141 (MQ=255)

       tatTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAAc                                                                                                                             >  2:88577/1‑141 (MQ=255)

           gTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTc                                                                                                                         >  1:55966/1‑141 (MQ=255)

           gTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTc                                                                                                                         >  1:718/1‑141 (MQ=255)

           gTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTGTCTACAAAACATTCTATTACAACTGTTTCTGAGTTGGACGGTTTTAACAGTc                                                                                                                         >  1:23387/1‑141 (MQ=255)

             tCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCAt                                                                                                                       <  2:25434/141‑1 (MQ=255)

              cTAATCTTTTTTTTTTTTTTTTTAGTATGAAATTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTTTTACTTTCTACAATACATTCTATTTCTTCTTTTTCTTATTTTTTCGGTTTTAACAGTCATa                                                                                                                      >  2:177866/1‑141 (MQ=255)

                 aTCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTATTAACAGTCATACaa                                                                                                                   <  2:166573/141‑1 (MQ=255)

                                   tGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTa                                                                                                 >  1:363305/1‑141 (MQ=255)

                                     aGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAg                                                                                               >  1:67890/1‑141 (MQ=255)

                                            aTTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACt                                                                                        <  1:181812/141‑1 (MQ=255)

                                                      ttattTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAg                                                                              <  2:15738/141‑1 (MQ=255)

                                                      ttattTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAg                                                                              >  1:243361/1‑141 (MQ=255)

                                                       tattTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGt                                                                             >  1:15643/1‑141 (MQ=255)

                                                       tattTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGt                                                                             <  1:28688/141‑1 (MQ=255)

                                                         ttttACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTcc                                                                           <  1:206063/141‑1 (MQ=255)

                                                                        aCTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTTCATTTTAGTCCTAAACAGTTCCGTTc                                                            >  2:337009/1‑141 (MQ=255)

                                                                          ttGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCAc                                                          <  1:175210/141‑1 (MQ=255)

                                                                           tGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACt                                                         >  2:21877/1‑141 (MQ=255)

                                                                             ttAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCg                                                       >  1:195376/1‑141 (MQ=255)

                                                                                       cAATTTATTACTTTCTACAAAACCTTCTATTACTACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATGACTTGCATGTTAGTCCTAAACAGTTTCGTTCACTCGTTTCCAAGAt                                             >  2:238511/1‑141 (MQ=255)

                                                                                         aTTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTa                                           <  2:11066/141‑1 (MQ=255)

                                                                                            tattaCTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTg                                        >  1:145789/1‑141 (MQ=255)

                                                                                            tattaCTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTg                                        >  1:198888/1‑141 (MQ=255)

                                                                                            tattaCTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTg                                        <  1:55275/141‑1 (MQ=255)

                                                                                                   ttCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAaccacc                                 <  1:337446/141‑1 (MQ=255)

                                                                                                           aaCATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATac                         >  2:249796/1‑141 (MQ=255)

                                                                                                           aaCATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATac                         <  1:365055/141‑1 (MQ=255)

                                                                                                               ttCTATTACAACTGTTTCTGAATTGGACGGTTTTAACTTTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACtt                     >  2:172974/1‑141 (MQ=255)

                                                                                                                tCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTc                    >  1:129680/1‑141 (MQ=255)

                                                                                                                 cTATTACTACTGTTTCTGAATTGGACGGTTTTAACAGTAATACAAATTGTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTCCCGTTCACTCGTTTCCAAGATTACACAACCACCACAAATACACTTcc                   <  2:119072/141‑1 (MQ=255)

                                                                                                                       cAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTACTCCTACACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAg             <  1:163924/141‑1 (MQ=255)

                                                                                                                                  gAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATca  <  2:253921/141‑1 (MQ=255)

                                                                                                                                  gAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATca  <  2:93873/141‑1 (MQ=255)

TGAATCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCA  >  CP000730/2502004‑2502274

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A