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	2,378,139	T→C	41.9%	P83P (CCA→CCG)	ubiB ←	2‑octaprenylphenol hydroxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,378,139	0	T	C	41.9%	16.7 / 45.0	62	P83P (CCA→CCG)	ubiB	2‑octaprenylphenol hydroxylase
Reads supporting (aligned to +/- strand): ref base T (17/19); new base C (11/15); total (28/34)
Fisher's exact test for biased strand distribution p-value = 7.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.29e-01

TCGCCAGCTTGCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGCCCCAGTTCTTGCA  >  minE/2378072‑2378206

tCGCCAGCTTGCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGt                                                                     >  1:3053372/1‑68 (MQ=255)

tCGCCAGCTTGCCATCAAACGGAGAAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGt                                                                     >  1:2874296/1‑68 (MQ=255)

         tGCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGAt                                                           >  1:539827/1‑69 (MQ=255)

          gCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATc                                                          >  1:1151664/1‑69 (MQ=255)

          gCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATc                                                          >  1:2127867/1‑69 (MQ=255)

          gCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATc                                                          >  1:2131875/1‑69 (MQ=255)

                  aCGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCggg                                                  >  1:870107/1‑69 (MQ=255)

                  aCGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCggg                                                  >  1:1608927/1‑69 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGTCGGaaa                                                                <  1:5417/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGTaaa                                                                <  1:2808308/53‑1 (MQ=38)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:595053/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:2018492/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:2022194/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:2700014/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:867093/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:575731/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:3177911/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:443911/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:468335/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:1995505/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:2014602/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGaaa                                                                <  1:970259/53‑1 (MQ=255)

                    ggAGCGACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGAGGCGGaaa                                                                <  1:2197104/53‑1 (MQ=255)

                             ttGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACAtt                                       >  1:809793/1‑69 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:1024256/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:473368/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:1282995/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:3050379/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:990107/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:1498291/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:2817896/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:2681585/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:2449564/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGcc                                   >  1:234372/1‑68 (MQ=255)

                                  cTGCAATAACGCCAGCTGATCGGCAATATGCGGCGGAAAAAGATCGCGGCGGGTTGATAACATCTGc                                    >  1:1681144/1‑67 (MQ=255)

                                         aaCGCCATCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:1232828/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAAc                                          <  1:2032273/54‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAAc                                          <  1:1115832/54‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAAc                                          <  1:515434/54‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAAc                                          <  1:1310305/54‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:1335455/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:1915610/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:3170121/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:2638241/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:1521164/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:1711190/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:261468/69‑1 (MQ=255)

                                         aaCGCCAGCTGATCGGCAATATCCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTg                           <  1:2607642/69‑1 (MQ=255)

                                          aCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGa                          >  1:1054541/1‑69 (MQ=255)

                                          aCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGa                          >  1:857941/1‑69 (MQ=255)

                                          aCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGa                          >  1:3392402/1‑69 (MQ=255)

                                          aCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGa                          >  1:3017250/1‑69 (MQ=255)

                                          aCGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGa                          >  1:19626/1‑69 (MQ=255)

                                               aGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:3175909/69‑1 (MQ=255)

                                               aGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:3093443/69‑1 (MQ=255)

                                               aGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:3075101/69‑1 (MQ=255)

                                               aGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:2401279/69‑1 (MQ=255)

                                               aGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:1900526/69‑1 (MQ=255)

                                                gCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCaa                     <  1:2574906/68‑1 (MQ=255)

                                                      cGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGc               >  1:2334663/1‑68 (MQ=255)

                                                      cGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGc               >  1:997139/1‑68 (MQ=255)

                                                             atGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGCCCCAGTTc       >  1:3001701/1‑69 (MQ=255)

                                                             atGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGCCCCAGTTc       >  1:1380625/1‑69 (MQ=255)

                                                                  gTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGCCCCAGTTCTTGCa  >  1:495779/1‑69 (MQ=255)

TCGCCAGCTTGCCATCAAACGGAGCAACTTTGTCCTGCAATAACGCCAGCTGATCGGCAATATGCGGTGGAAAAAGATCGCGGCGGGTTGATAACATTTGCCCGAACTTGATCCAAACCGGCCCCAGTTCTTGCA  >  minE/2378072‑2378206

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