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
A8 F110 I2 R1	16	53.0	1914758	91.2%	1746259	142.7

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	97.1%	85.5 / NA	36	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 (21/13); minor base G (0/1); total (22/14)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGTT  >  NC_000913/1196170‑1196444

aaaGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTgat                                                                                                                                      >  1:902736/1‑143 (MQ=255)

        tCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGCCTGATGGATGgcg                                                                                                                              >  2:180056/1‑143 (MQ=255)

           tGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCCCTa                                                                                                                           >  2:88372/1‑143 (MQ=255)

           tGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACGTCGAGTGTCTGATGGATGGCGCTa                                                                                                                           >  2:734643/1‑143 (MQ=255)

               tctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGACAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAAct                                                                                                                       >  2:815584/1‑143 (MQ=255)

                 tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTCAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAActgc                                                                                                                     >  2:546044/1‑143 (MQ=255)

                 tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAACTATGACTTCGAGTGTCTGATGGATGGCGCTAAActgc                                                                                                                     >  2:480737/1‑143 (MQ=255)

                         tctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGt                                                                                                             >  1:809542/1‑143 (MQ=255)

                            ccGCTGAGAGGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGAAGGATGGCGCTAAACTGCTGAAATGTTCa                                                                                                          <  1:631900/143‑1 (MQ=255)

                              gCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                                                                                        >  1:513245/1‑143 (MQ=255)

                              gCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                                                                                        >  1:513115/1‑143 (MQ=255)

                                    atgatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAAACAACGCGAACACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTGCAGAGTATgg                                                                                                  >  2:310270/1‑143 (MQ=18)

                                           tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTACTTGTTAACGGTCTGGAAGGCGCAATCAACGCGAAAACCATAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                                                                           >  1:540677/1‑143 (MQ=18)

                                           tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                                                                                           >  1:234554/1‑143 (MQ=255)

                                                      ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                                                                                >  1:18985/1‑143 (MQ=255)

                                                               gAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATg                                                                       <  2:717548/143‑1 (MQ=255)

                                                                 aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAAGCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGAGCGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGAGTATTGTTTATCGAAAACATGTAATGcc                                                                     <  2:581262/143‑1 (MQ=17)

                                                                        gACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGttt                                                              <  1:836963/143‑1 (MQ=255)

                                                                           ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGtt                                                           >  2:273117/1‑143 (MQ=255)

                                                                                   taaaataaTGGAAGGCGCAATCAATGCGCAAACCGTAACATATGACTTCGAGTGTGTGATGGATGGCGCTAAACCGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttat                                                   <  1:346223/136‑1 (MQ=18)

                                                                                        gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGACATGTTCAGAGTTTGGTGACGCGAGCATCGAAAACATGTAATGCCGTAGTTTGTTAACTTTATTGACg                                              >  1:280250/1‑143 (MQ=21)

                                                                                        gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACg                                              >  1:593334/1‑143 (MQ=255)

                                                                                         tATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACgg                                             <  1:23015/143‑1 (MQ=255)

                                                                                                  cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAAc                                    >  1:197860/1‑143 (MQ=255)

                                                                                                          aCGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCAgt                            >  2:394020/1‑143 (MQ=255)

                                                                                                             cgAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCgttgt                         <  1:573822/143‑1 (MQ=255)

                                                                                                                 aatcGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGttttt                     <  2:456867/140‑1 (MQ=255)

                                                                                                                  aCCGTAACCTAGGACTTCGAGGGTCTGATGGATGGCGCTAAACGGCTGAAATGTTCAGAGTTGGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGtttttt                    <  2:922125/143‑1 (MQ=255)

                                                                                                                  aCCGGAACCTATGATGTCGAGTGTCGGATGGATGGCGCTAAACTGCTGAAATGTTCAGCGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGtttttt                    <  2:305539/143‑1 (MQ=37)

                                                                                                                      tAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTa                >  2:669385/1‑143 (MQ=255)

                                                                                                                        aCCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAgg              <  1:340552/143‑1 (MQ=255)

                                                                                                                        aCCTATGACTTCGAGTGTCTGAAGGATGGCGCTAAACTGCTTGAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAgg              <  1:915436/143‑1 (MQ=255)

                                                                                                                             tGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTCTTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgctgct         >  2:749095/1‑143 (MQ=255)

                                                                                                                                 ttCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACg     >  1:885502/1‑143 (MQ=255)

                                                                                                                                    gAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGtt  <  2:513115/143‑1 (MQ=255)

                                                                                                                                    gAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGtt  <  2:513245/143‑1 (MQ=255)

AAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGTT  >  NC_000913/1196170‑1196444

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