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
A24 F106 I2 R1	20	33.2	1150230	93.5%	1075465	143.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,604,632	C→A	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,604,632	0	C	A	97.7%	136.5 / NA	43	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (21/21); total (22/21)
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

GACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTT  >  NC_000913_3_pae_tpiA/4604494‑4604772

gacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTAGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAACAGCAATAGCAAAACGATCCGTGCAACTAAAttg                                                                                                                                    >  1:121120/1‑148 (MQ=255)

   tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                 <  1:217216/149‑1 (MQ=255)

    gAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAtg                                                                                                                                >  1:54182/1‑149 (MQ=255)

     aaCAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAtgt                                                                                                                               <  2:212317/149‑1 (MQ=255)

         aTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATg                                                                                                                           >  1:159600/1‑149 (MQ=255)

              tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaa                                                                                                                      >  1:239099/1‑149 (MQ=255)

              tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCCTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCACTATCAAAACAAACCGTGAACATAAATTTAATTTTATGTccca                                                                                                                      >  2:93392/1‑146 (MQ=255)

                gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAc                                                                                                                    >  2:385573/1‑149 (MQ=255)

                   cATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTgg                                                                                                                 <  1:168823/149‑1 (MQ=255)

                   cATTAACCAAAGCCGGACGTGAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTgg                                                                                                                 <  1:93392/149‑1 (MQ=255)

                    aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGACGAACAGCTTAAACGCAATATCAAGACAATCCGTGAACAGAATTTTAATGTCATGTAGGAACTggg                                                                                                                >  2:437462/1‑149 (MQ=255)

                                       tAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAggg                                                                                             <  2:231052/149‑1 (MQ=255)

                                           cccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgt                                                                                         <  1:490017/149‑1 (MQ=255)

                                            ccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgtt                                                                                        <  1:225446/149‑1 (MQ=255)

                                             cgcgggAGTGAGAAATATTGCGCTTTATGTCGCGGTGATACTCAATGACACAAATTGCGTAGTAGTTTAATCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGttgttg                                                                                       <  1:150820/145‑1 (MQ=255)

                                               aCGGAAAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                     <  2:516294/149‑1 (MQ=255)

                                                         aaaTATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCATTATCAGAACGAACCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCGGTGTTGTTGGCGGCTGCAGat                                                                           >  2:156737/1‑149 (MQ=255)

                                                         aaaTATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTTGAGGCCGCAGag                                                                           >  2:247659/1‑148 (MQ=255)

                                                             atTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                       <  2:219993/149‑1 (MQ=255)

                                                              ttGCGCTTTAGGTCGCGTGGCTACTCAATGACACGAATTGCCGAGCAGCTTAAACTCAATATCTAAACGATCCGTGAACATAAATTGAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCt                                                                      <  1:511684/149‑1 (MQ=255)

                                                               tGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTg                                                                     <  1:57567/149‑1 (MQ=255)

                                                                  gcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                  <  2:239099/149‑1 (MQ=255)

                                                                    tttATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGAAATTTTAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatg                                                                >  1:542209/1‑149 (MQ=255)

                                                                           cgcgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTGGTTGGAGGCCGCAGATATTCTGTTATGTATGCgg                                                         >  1:98441/1‑149 (MQ=255)

                                                                             cgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCa                                                       <  1:56653/149‑1 (MQ=255)

                                                                              gTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCAt                                                      >  1:384235/1‑149 (MQ=255)

                                                                                   tACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGa                                                 >  2:73277/1‑149 (MQ=255)

                                                                                        aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                            >  1:534361/1‑149 (MQ=255)

                                                                                        aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGGATGCGGCATTGCGAAACaa                                            >  1:464496/1‑149 (MQ=255)

                                                                                              acaAATTGCCGAGCAGCTTAAACGCAAAATAAAAACGGTCCGTGAACCTAGATTTAATGTGATGTCGAAACTTGGCGTCAGTTCTGCCGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtg                                      <  1:29213/149‑1 (MQ=255)

                                                                                                aaaTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGGGATGTCGAAAATGGGCGTCAATTCTGACGCAGGGTTATGGGAGGACGCAGATATGCAGATATGTATGCGGCATTGCGAAACAAGTAAtgtg                                    >  2:238545/1‑149 (MQ=255)

                                                                                                aaaTTGCCAAGCAGCTTAAACACCATCTCAAAACTGTCCGGGAACATAAGATGAATGTGATTTCGTAAGTGGGCGTCAGTGCTGACGCAGGGTGGTTGGAGGCCGCAGATGTTCTGTTATGTATGCGGCATTGCGAAACAAGTAGtgtg                                    >  2:52294/1‑149 (MQ=255)

                                                                                                  aTTGCCGAGCAGCTTAAAAGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                  <  2:54182/149‑1 (MQ=255)

                                                                                                       cGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTg                                                                     <  2:570248/109‑1 (MQ=255)

                                                                                                       cGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTg                                                                     >  1:570248/1‑109 (MQ=255)

                                                                                                       cGAGCAGCGTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGTCGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTCAGATGGATACTGTGCGAAACAAGTAATGTGTTGCATc                             <  2:555464/149‑1 (MQ=255)

                                                                                                         agcagcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATccc                           >  1:290484/1‑149 (MQ=255)

                                                                                                            agcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                        >  1:372301/1‑149 (MQ=255)

                                                                                                                        atatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                        >  1:524182/1‑137 (MQ=255)

                                                                                                                        atatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                        <  2:524182/137‑1 (MQ=255)

                                                                                                                             aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                  >  2:398842/1‑122 (MQ=255)

                                                                                                                             aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                  <  1:398842/122‑1 (MQ=255)

                                                                                                                                  gATCCGGGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACGAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGttt  <  1:165941/149‑1 (MQ=255)

GACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTT  >  NC_000913_3_pae_tpiA/4604494‑4604772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A