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 F108 I1 R1	11	40.8	1469306	91.3%	1341476	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,196,305	C→T	R395C (CGT→TGT)	icd →	isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,305	0	C	T	95.0%	97.4 / NA	42	R395C (CGT→TGT)	icd	isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase
Reads supporting (aligned to +/- strand): ref base C (1/0); major base T (18/20); minor base A (2/0); total (21/21)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGTT  >  NC_000913/1196167‑1196444

taCAAAGTTAATTCTGGCTCTATTATTCTATCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCt                                                                                                                                         <  2:713311/142‑1 (MQ=255)

   aaaGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACAGCAACCTATGACTAAGAGAGTCtaaa                                                                                                                                      >  1:400899/1‑140 (MQ=37)

      gTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTgatgga                                                                                                                                   <  2:269760/143‑1 (MQ=255)

               ggttctATTATGCGCTCGGCGGAGATGATGCGGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTaa                                                                                                                          <  2:576475/140‑1 (MQ=21)

                tctctATTATTCTATCCGCTGTTATGATGCTGCGCCACATGGGGAGGACCGAAGCGGCTGACTTAATTATTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTaaa                                                                                                                         <  2:378084/142‑1 (MQ=21)

                     gttagcctctgCGCTGAGATGAGGCTGCGCCAGATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAActgct                                                                                                                    <  2:116718/137‑1 (MQ=21)

                            tctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGACATGt                                                                                                             >  2:252591/1‑143 (MQ=255)

                            tctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGt                                                                                                             >  2:462049/1‑143 (MQ=255)

                            tctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTCAGAGAGTCTGATGGATGGCACTAAACTGCCGAAAAGt                                                                                                             >  1:281788/1‑143 (MQ=21)

                             ctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCACTCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCACAACTCCTGAAATgat                                                                                                            >  2:181568/1‑141 (MQ=21)

                              tcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCACTCAACGTGAAAGTCGTAAGCTCTGTCCCCGACTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTc                                                                                                           >  2:265562/1‑143 (MQ=21)

                              tcCGCTGAGATGAGGCTGCGCCACATGGGGTGGACCGACGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTc                                                                                                           <  2:434496/143‑1 (MQ=255)

                                 gCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                                                                                        >  2:31706/1‑143 (MQ=255)

                                      gagggtgctggACCACAAGGGTTGGTACGAAGCGGCTGAATTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg                                                                                                   <  1:336487/138‑1 (MQ=18)

                                       acgacgctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCGGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTgg                                                                                                  <  1:644050/138‑1 (MQ=255)

                                               gcgcCACTTTGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGa                                                                                          >  1:682260/1‑143 (MQ=255)

                                                    acaTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGAAATCAACGCGAAAACCGTAACCTATGACTACGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTAAGAGGTTGGTGACGAGaacatg                                                                                     >  1:228948/1‑142 (MQ=18)

                                                                ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                                                                         >  2:430634/1‑143 (MQ=255)

                                                                              ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGtt                                                           >  2:682325/1‑143 (MQ=255)

                                                                                 aTTGTTGAAGGTATGGAGGGCGCAATCAACGTGAAAACCGTAACCTATGACTTCGAGTGTCAGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaaa                                                        <  1:54384/143‑1 (MQ=18)

                                                                                  tgcgtacaagTACGGAAGGCGCAATCAACGCGATACCCTTAACCTATGCCTTCGCTTGTCTTATGGATAGCGCTAAACGCCTGAAATGCTCAGATTGTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAt                                                       <  2:87002/134‑1 (MQ=16)

                                                                                    gTTATAGGTATGGAGGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGGTGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt                                                     <  2:546807/143‑1 (MQ=255)

                                                                                      tAAAGGTGTGGAAGGCGCAATCAAATCGAAAACCGTAATCTATGACTTCGAGTGTCTGATGGATGGCGCAAAACGGCGGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttat                                                   <  2:352338/143‑1 (MQ=18)

                                                                                         atgTATGGAAGGCGGAATCAACGCGAAAAGCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACGGCTGAAATGTTCAGAGTGTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTaa                                                <  2:288412/141‑1 (MQ=21)

                                                                                          ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAAc                                               >  2:580207/1‑143 (MQ=255)

                                                                                            tATGGAGGGCGCAATCAACGCGAAATCCGTCACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTTCTGAAGTGTTCAGAGTTTGGTGACGCGATCATCGATATCATGTAATGCCGTTGTTTGTTAAATTTATTAACgg                                             <  1:575490/143‑1 (MQ=255)

                                                                                              tGGGAGGCGCAATCAACGCAAAAACCGTATCCTATGACTGCGAGTGTCTGATGGATGGCGCTCAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGa                                           <  1:345657/143‑1 (MQ=21)

                                                                                                gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGCAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAACTTTATTAACGGGAGc                                         >  1:523467/1‑143 (MQ=255)

                                                                                                        aaTCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGAGCATCGATAACATGTAGTGCCGTAGTTTGTTAAATTTATTAATGAGAGCGTAAAGCt                                 >  2:235737/1‑143 (MQ=25)

                                                                                                          tCAACGCGAAAACCGTAACCTATTACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTTACGCTcc                               <  1:47365/143‑1 (MQ=255)

                                                                                                          tCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTATCGGGAGCGGAACGCTcc                               >  2:262567/1‑143 (MQ=255)

                                                                                                          tCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTTACGCTcc                               <  1:399467/143‑1 (MQ=255)

                                                                                                           cAAGGCGAAGACCGTAGCCTAAGACTGCGAGGGGCTGATGGGTGGCGCGAAACTGCTGAAATGTTCAGAGTTGGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTccc                              <  2:682260/143‑1 (MQ=25)

                                                                                                             aCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGGTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAAGGCCCCCgt                            >  2:535900/1‑143 (MQ=255)

                                                                                                                    aaCCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGatttt                     >  2:671576/1‑143 (MQ=255)

                                                                                                                     aCCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCCTTGtttttt                    <  1:682325/143‑1 (MQ=255)

                                                                                                                         tAACCTTTGACTTCGATTGGCTGATGGTTGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTTACGCTCCCgttaataaatttaa                <  2:647160/143‑12 (MQ=21)

                                                                                                                         tAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTa                <  2:621468/143‑1 (MQ=255)

                                                                                                                            ccTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgc             >  2:445236/1‑143 (MQ=255)

                                                                                                                              tATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGAACGGCGAAAACATGTGCTGGCGTAGGCGGTTAGCTTTATTAACCGACGCGTAACGCGCCCGTTGTTTTTTGttgcgccg           >  2:162926/1‑137 (MQ=18)

                                                                                                                                    ttCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTACTGCCGTAGTTTGTTAAATTTATTAACGAGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCAGCTAACg     >  2:446740/1‑143 (MQ=255)

                                                                                                                                       gAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTACCGGtt  >  1:716787/1‑143 (MQ=255)

GACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGTT  >  NC_000913/1196167‑1196444

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A