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 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,325,916	A→G	N402D (AAT→GAT)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,325,916	0	A	G	83.0%	144.5 / 21.6	60	N402D (AAT→GAT)	atoS	sensory histidine kinase in two‑component regulatory system with AtoC
Reads supporting (aligned to +/- strand): ref base A (10/0); new base G (19/30); total (29/31)
Fisher's exact test for biased strand distribution p-value = 3.19e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.35e-01

TGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAT  >  W3110S.gb/2325851‑2325981

tGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCg                                                              >  1:3262044/1‑71 (MQ=255)

tGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCg                                                              >  1:2446137/1‑71 (MQ=255)

tGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCg                                                              >  1:917588/1‑71 (MQ=255)

tGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCg                                                              >  1:1893632/1‑71 (MQ=255)

        gCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGc                                                      <  1:2126728/71‑1 (MQ=255)

        gCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGc                                                      <  1:623458/71‑1 (MQ=255)

          aGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTa                                                    <  1:2684752/71‑1 (MQ=255)

          aGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTa                                                    <  1:3513678/71‑1 (MQ=255)

          aGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTa                                                    <  1:3659833/71‑1 (MQ=255)

          aGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTa                                                    <  1:173246/71‑1 (MQ=255)

           gAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:799509/71‑1 (MQ=255)

           gAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:2875977/71‑1 (MQ=255)

           gAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:2246838/71‑1 (MQ=255)

           gAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:1028874/71‑1 (MQ=255)

           gAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:984120/71‑1 (MQ=255)

                    gCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGt                                            <  1:1775128/69‑1 (MQ=255)

                    gCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGt                                            <  1:2695671/69‑1 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAAc                                                         >  1:1496675/1‑54 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:3106764/1‑69 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:1484123/1‑69 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:147130/1‑69 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:1424454/1‑69 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:1359191/1‑69 (MQ=255)

                      cacaCTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:2615109/1‑69 (MQ=255)

                      aacacTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTa                                          >  1:2870264/2‑69 (MQ=255)

                                   cTGATGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTgcg                           <  1:1534133/71‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3428233/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:572486/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:75565/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:459238/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3990267/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3878885/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3481063/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3448444/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:3380686/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:2836749/70‑1 (MQ=255)

                                      aTGGCTGGCGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGcc                         <  1:2292663/70‑1 (MQ=255)

                                          ctggcGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCcaacaa                    <  1:2214483/71‑1 (MQ=255)

                                          ctggaGTCGCGCATGAAGTACGTTATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCcaacaa                    <  1:841467/71‑1 (MQ=255)

                                             gcGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAAcc                 <  1:3341337/71‑1 (MQ=255)

                                             gcGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAAcc                 <  1:1653375/71‑1 (MQ=255)

                                             gcGTCGCGCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAAcc                 <  1:2238997/71‑1 (MQ=255)

                                               gTCGCGCATGAAGTACGTGATCCGTTAACGGCTAt                                                   <  1:1152935/35‑1 (MQ=255)

                                                 cgcgCATGAAGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGt              >  1:2952384/1‑70 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:1718751/1‑57 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:798421/1‑57 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:268338/1‑57 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:2867546/1‑57 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:28855/1‑57 (MQ=255)

                                                         aaGTACGTGATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACaaa                   >  1:1444425/1‑57 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATc                                >  1:553348/1‑39 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:3631209/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:579785/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:503949/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:473728/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:3678331/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:2020901/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:2160127/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:2367186/1‑69 (MQ=255)

                                                              cGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAt  >  1:2537553/1‑69 (MQ=255)

TGGCGCAAGCAGAACGCCTCGCCACACTGGGTGAGCTGATGGCTGGCGTCGCGCATGAAGTACGTAATCCGTTAACGGCTATTCGTGGTTATGTACAGATCTTGCGCCAACAAACCAGTGACCCAATACAT  >  W3110S.gb/2325851‑2325981

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