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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,951,452	C→T	pseudogene (893/984 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,951,452	0	C	T	100.0%	123.4 / NA	33	pseudogene (893/984 nt)	ilvG	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (11/22); total (11/22)

GGATGCACGGCACCAAAGCGGCAAACTTCGCGGTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGCAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCTGGCGTT  >  NC_000913/3951305‑3951590

ggATGCACGGCACCAAAGCGGCAAACTTCGCGGTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGa                                                                                                                                         <  2:573025/151‑1 (MQ=255)

  aTGCACGGCACCAAAGCGGCAAACTTCGCGGTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGaa                                                                                                                                        >  2:350167/1‑150 (MQ=255)

                    gCAAACTTCGCGGTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAgg                                                                                                                     >  1:134621/1‑151 (MQ=255)

                               ggTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGc                                                                                                           >  1:463575/1‑150 (MQ=255)

                                        gtgtGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGt                                                                                                 <  1:231186/151‑1 (MQ=255)

                                             aCCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGAttt                                                                                            <  1:96138/151‑1 (MQ=255)

                                                    gATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGc                                                                                      <  1:436585/150‑1 (MQ=255)

                                                       cGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTg                                                                                  <  1:290653/151‑1 (MQ=255)

                                                           gTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTAc                                                                              <  1:350164/151‑1 (MQ=255)

                                                             gggCGCACGGTGTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGt                                                                                 <  1:204448/146‑1 (MQ=255)

                                                                 gcACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCAt                                                                        <  1:520811/151‑1 (MQ=255)

                                                                  cACGTTTTGATGACCGGGTGACCGGCAAACTGAACCCCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCAtt                                                                       <  1:356284/151‑1 (MQ=255)

                                                                         tgatgaCCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTAcagca                                                                 <  2:566561/150‑1 (MQ=255)

                                                                           atgaCCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGcc                                                              >  1:108977/1‑151 (MQ=255)

                                                                                cGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTaa                                                         <  2:27218/151‑1 (MQ=255)

                                                                                 gggTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTaaa                                                        <  2:650668/151‑1 (MQ=255)

                                                                                     gACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCa                                                     <  2:171982/150‑1 (MQ=255)

                                                                                                 gAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGgcag                                          <  2:163914/149‑1 (MQ=255)

                                                                                                  aaCACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGgcagca                                        >  1:446044/1‑150 (MQ=255)

                                                                                                           gcgcCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTgcgcg                              <  1:628857/151‑1 (MQ=255)

                                                                                                            cgcCACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTgcgcgc                             <  1:104647/151‑1 (MQ=255)

                                                                                                              ccACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTgcgcgc                             >  1:148189/1‑149 (MQ=255)

                                                                                                              ccACACGCCAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAg                           <  2:228388/151‑1 (MQ=255)

                                                                                                                     ccAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGtg                    >  2:315651/1‑151 (MQ=255)

                                                                                                                      cAGTGTTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGtga                   <  1:513238/151‑1 (MQ=255)

                                                                                                                        gtgtTATCCATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGtgatg                 <  2:167697/151‑1 (MQ=255)

                                                                                                                               ccATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTc          >  1:523790/1‑151 (MQ=255)

                                                                                                                                cATATGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTcc         >  2:83903/1‑151 (MQ=255)

                                                                                                                                 atatGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCt        >  1:592520/1‑151 (MQ=255)

                                                                                                                                 atatGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCt        <  1:257178/151‑1 (MQ=255)

                                                                                                                                   atGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCTgg      <  2:463579/151‑1 (MQ=255)

                                                                                                                                   atGGATATCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCTgg      <  1:122838/151‑1 (MQ=255)

                                                                                                                                       atatCGACCCGGTAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCTGGCGtt  >  2:120326/1‑151 (MQ=255)

GGATGCACGGCACCAAAGCGGCAAACTTCGCGGTGCAGGAGTGTGACCTGCTGATCGCCGTGGGCGCACGTTTTGATGACCGGGTGACCGGCAAACTGAACACCTTCGCGCCACACGCCAGTGTTATCCATATGGATATCGACCCGGCAGAAATGAACAAGCTGCGTCAGGCACATGTGGCATTACAAGGTGATTTAAATGCTCTGTTACCAGCATTACAGCAGCCGTTAAATCAATGACTGGCAGCAACACTGCGCGCAGCTGCGTGATGAACATTCCTGGCGTT  >  NC_000913/3951305‑3951590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A