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
A5 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	711,161	C→T	34.4%	intergenic (‑93/+196)	fur ← / ← fldA	DNA‑binding transcriptional dual regulator/flavodoxin 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	711,161	0	C	T	34.4%	70.2 / 57.8	61	intergenic (‑93/+196)	fur/fldA	DNA‑binding transcriptional dual regulator/flavodoxin 1
Reads supporting (aligned to +/- strand): ref base C (22/18); new base T (12/9); total (34/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

TCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTACATTTAC  >  W3110S.gb/711096‑711228

tCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCt                                                                 >  1:5063359/1‑70 (MQ=255)

 cACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa                                                                >  1:51200/1‑70 (MQ=255)

 cACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa                                                                <  1:51215/70‑1 (MQ=255)

 cACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa                                                                >  1:1962920/1‑70 (MQ=255)

 cACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa                                                                <  1:4704371/70‑1 (MQ=255)

  aCTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa                                                                <  1:4010067/69‑1 (MQ=255)

     tCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATg                                                            >  1:157651/1‑70 (MQ=255)

      cATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGa                                                           >  1:1839581/1‑70 (MQ=255)

      cATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGa                                                           >  1:4744609/1‑70 (MQ=255)

       aTTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGaa                                                          <  1:3322045/70‑1 (MQ=255)

            aagaagTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACcac                                                    <  1:458537/71‑1 (MQ=255)

                   gACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTccc                                             >  1:3413063/1‑71 (MQ=255)

                    aCAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGaa                                                          <  1:751039/57‑1 (MQ=255)

                      aGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTgg                                          >  1:4807022/1‑71 (MQ=255)

                       gAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGc                                         <  1:3407012/71‑1 (MQ=255)

                          tttGCTCTTGAGATAATGCGTATCATTATTGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCaaa                                      <  1:1523651/71‑1 (MQ=255)

                          tttGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCaaa                                      <  1:4798343/71‑1 (MQ=255)

                             gCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAata                                    <  1:4243357/70‑1 (MQ=255)

                              ctctTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAatat                                   <  1:4917902/70‑1 (MQ=255)

                               tctTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCaa                                       <  1:3125908/65‑1 (MQ=255)

                                   gagaTTATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGtt                               <  1:3676260/69‑1 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGtt                               <  1:2387781/69‑1 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGtt                               <  1:887239/69‑1 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTaaa                                                              >  1:2811289/1‑38 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTaaa                                                              >  1:919581/1‑38 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTAAATGaa                                                          >  1:4179593/1‑42 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTAAATGaa                                                          >  1:3165209/1‑42 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTtaa                             >  1:450881/1‑71 (MQ=255)

                                   gagaTAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTtaa                             >  1:696147/1‑71 (MQ=255)

                                        aaTGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATaaa                         >  1:2311117/1‑70 (MQ=255)

                                         aTGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTcc                                              >  1:3586951/1‑48 (MQ=255)

                                          tGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCt                                            <  1:292518/49‑1 (MQ=255)

                                           gCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACg                     >  1:405018/1‑71 (MQ=255)

                                           gCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACg                     >  1:2241232/1‑71 (MQ=255)

                                            cGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACaa                                                  >  1:5099495/1‑41 (MQ=255)

                                            cGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACaa                                                  >  1:1498760/1‑41 (MQ=255)

                                               aTCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTta                              <  1:1622300/58‑1 (MQ=255)

                                                tCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGt                    <  1:1254837/67‑1 (MQ=255)

                                                tCATTATAGAATTGCCACGCCTAAATGAAAACcac                                                    >  1:948626/1‑35 (MQ=255)

                                                tCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGt                                                >  1:4327892/1‑39 (MQ=255)

                                                 cATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAat                                     <  1:563138/49‑1 (MQ=255)

                                                 cATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATaaaaa                       >  1:359937/1‑63 (MQ=255)

                                                  aTTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCaaa                                      >  1:2511978/1‑47 (MQ=255)

                                                  aTTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca                >  1:1683640/1‑69 (MQ=255)

                                                  aTTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca                >  1:179467/1‑69 (MQ=255)

                                                  aTTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAAc                      >  1:4874416/1‑63 (MQ=255)

                                                  aTTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca                >  1:5014678/1‑69 (MQ=255)

                                                  aTTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca                >  1:2512956/1‑69 (MQ=255)

                                                   ttATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAg             <  1:309803/71‑1 (MQ=255)

                                                   ttATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAg             <  1:1865755/71‑1 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGtt                               >  1:2258952/1‑50 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGtt                               >  1:4131212/1‑50 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATaaa                         <  1:720905/56‑1 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATaaa                         <  1:4396778/56‑1 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTg                   >  1:3999268/1‑62 (MQ=255)

                                                      taGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTg                   >  1:781581/1‑62 (MQ=255)

                                                        gAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTa         <  1:2035562/70‑1 (MQ=255)

                                                         aaTTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAata                                    <  1:4925735/42‑1 (MQ=255)

                                                             gCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATaaaaa                       >  1:3112495/1‑51 (MQ=255)

                                                              ccACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTACATTTAc  <  1:5069528/71‑1 (MQ=255)

                                                              ccACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTACATTTAc  <  1:1976699/71‑1 (MQ=255)

TCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTACATTTAC  >  W3110S.gb/711096‑711228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A