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 I1 R1	300	54.7	1718999	98.4%	1691495	149.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,040,408	C→T	intergenic (+32/+8)	fldB → / ← cptA	flavodoxin 2/toxin of CptAB toxin‑antitoxin pair

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,040,408	0	C	T	97.7%	143.6 / ‑3.9	44	intergenic (+32/+8)	fldB/cptA	flavodoxin 2/toxin of CptAB toxin‑antitoxin pair
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (21/21); total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.46e-01

GGGCAACTGTTCGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGCTCTTA  >  NC_000913/3040260‑3040551

gggCAACTGTTCGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGt                                                                                                                                               >  1:259067/1‑151 (MQ=255)

        gTTCGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGAGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCatctt                                                                                                                                         >  2:588010/1‑149 (MQ=255)

          tCGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCatctttat                                                                                                                                      <  2:634643/150‑1 (MQ=255)

           cGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCatctttatct                                                                                                                                    <  1:568433/151‑1 (MQ=255)

              gggTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTg                                                                                                                                 <  2:472977/151‑1 (MQ=255)

                  cTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGtc                                                                                                                             >  2:289713/1‑151 (MQ=255)

                      cgcTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCtt                                                                                                                         <  1:757759/151‑1 (MQ=255)

                          ggATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCttgt                                                                                                                       <  1:205705/149‑1 (MQ=255)

                            aTGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGca                                                                                                                   <  1:461052/151‑1 (MQ=255)

                             tGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGca                                                                                                                   >  2:39007/1‑150 (MQ=255)

                              gAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGcaa                                                                                                                  <  1:633845/150‑1 (MQ=255)

                                 aCTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGcaacaa                                                                                                               >  2:595026/1‑150 (MQ=255)

                                             gcccTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGTTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTaaa                                                                                                  <  1:367054/149‑1 (MQ=255)

                                             gACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTAGCGTCTCTTGTTGCAACAAAATCCGCCGTaa                                                                                                   >  2:633039/1‑150 (MQ=255)

                                             gACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCGTAACGAAAAGGCAGAGCATTACGCCTGATCTCCCTGACGGATGAGCGCAAATGCTTTGCGGTAATCTTTACCTGTGCGCCTCTTGTTCCAACAATAAccgttgtga                                                                                                   <  1:323483/150‑7 (MQ=255)

                                                  tAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATccc                                                                                              >  1:297795/1‑150 (MQ=255)

                                                  tAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATcc                                                                                               <  2:94858/149‑1 (MQ=255)

                                                       acgaGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCAtt                                                                                        >  2:759602/1‑151 (MQ=255)

                                                         gaGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTc                                                                                       >  1:682176/1‑150 (MQ=255)

                                                           gCGTATTCAGAGCTGGTGCGAGCAAATCCCCACCGAAATGGCAGAGCATTCCGCCTGATCTCACTGACGGCTTAGCGCTTATGCTTTGCTGTCATCTTTATCTTTGCGTCTTTTTTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAg                                                                                     <  2:2905/150‑1 (MQ=255)

                                                             gTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCtt                                                                                  >  2:652729/1‑151 (MQ=255)

                                                               aTTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGAATATGCTTTGCTGTCATCTTTATCTTGGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTc                                                                                 <  2:383752/150‑1 (MQ=255)

                                                                ttCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGt                                                                               >  1:752950/1‑151 (MQ=255)

                                                                ttCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTGGCGTCTCTTTTTGCAACAAAACCCGCCGTAAATCCCGCCATTCAGCTTc                                                                                 <  1:558727/149‑1 (MQ=255)

                                                                       cTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATg                                                                          <  2:452711/149‑1 (MQ=255)

                                                                          gTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTc                                                                     <  2:823327/151‑1 (MQ=255)

                                                                              gAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCt                                                                 >  2:552627/1‑151 (MQ=255)

                                                                                  aaaTCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCAGCTgcca                                                             <  2:687856/151‑1 (MQ=255)

                                                                                      ccTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTgccagcca                                                         <  2:747320/151‑1 (MQ=255)

                                                                                          aaCGAAATGGCAGAGCATTCCGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATaa                                                      <  2:639808/150‑1 (MQ=255)

                                                                                          aaCGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATaa                                                      >  2:437290/1‑150 (MQ=255)

                                                                                             gAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGt                                                  >  1:666060/1‑151 (MQ=255)

                                                                                              aaaTGGCAGAGCTTTCCCCCTGTTCTCACTGACGGGTTAGCCCAAATGCTTTCCTGTCATCTTTATCTTGGCGTCTCTTGTTGCAACAAAACCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATg                                                   <  1:663657/149‑1 (MQ=255)

                                                                                              aaaTGGCAGAGCATTACGCCTGATCCCCCTGACGGCTTAGCGCATACGCTTTGCTGTCATCTTTATTTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGtt                                                 <  1:388069/151‑1 (MQ=255)

                                                                                                aTGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGc                                               >  2:752201/1‑151 (MQ=255)

                                                                                                     agagCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt                                          >  1:457514/1‑151 (MQ=255)

                                                                                                     agagCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGttt                                          >  2:413202/1‑151 (MQ=255)

                                                                                                              cGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCa                                   <  2:339543/149‑1 (MQ=255)

                                                                                                                ccTGATCTCACTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTGGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAg                               <  1:308492/151‑1 (MQ=255)

                                                                                                                          cTGACGGCTTAGCGCATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACg                     >  1:506383/1‑151 (MQ=255)

                                                                                                                                        cATATGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGc       >  1:832601/1‑151 (MQ=255)

                                                                                                                                         atatGCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGct      >  1:15284/1‑151 (MQ=255)

                                                                                                                                             gCTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGCTCtt   >  1:218679/1‑150 (MQ=255)

                                                                                                                                              cTTTGCTGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGCTCTTa  >  1:255774/1‑150 (MQ=255)

GGGCAACTGTTCGTGGGTCTGGCGCTGGATGAAACTAACCAGTATGACCTTAGCGACGAGCGTATTCAGAGCTGGTGCGAGCAAATCCTCAACGAAATGGCAGAGCATTACGCCTGATCTCACTGACGGCTTAGCGCATATGCTTTGCCGTCATCTTTATCTTTGCGTCTCTTGTTGCAACAAAATCCGCCGTAAATCCCGCCATTCAGCTTCGTCCATGCTGTCGGCTGCCAGCCATAAATGTTGCCGTTTACCGCCATCAGAACGTAAACGCAGCATCATGCCGCTCTTA  >  NC_000913/3040260‑3040551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A