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 F44 I1 R1	27	48.3	2078744	90.6%	1883342	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	710,489	G→C	A53G (GCT→GGT)	fur ←	DNA‑binding transcriptional dual regulator Fur

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	710,489	0	G	C	97.7%	125.2 / NA	43	A53G (GCT→GGT)	fur	DNA‑binding transcriptional dual regulator Fur
Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (25/17); total (25/18)
Fisher's exact test for biased strand distribution p-value = 4.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTTGCCGCAGTCGAGGCAGATCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGG  >  NC_000913/710352‑710626

tcTTGCCGCAGGCGAGGCAGATAGGGTGAGCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATGGTGGCGGGTGACGATGCCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGa                                                                                                                                      <  2:247505/142‑1 (MQ=255)

      cGCAGTCGAGGCAGATCAGGTGATCGTGGTGATGTGGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAAtt                                                                                                                                >  1:712933/1‑143 (MQ=255)

           tggAGGCAGATCAGGTGATCGGGGTGAGGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATttcttc                                                                                                                           <  1:679605/141‑1 (MQ=255)

           tCGAGGCAGATCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCACTttcttc                                                                                                                           >  2:78805/1‑143 (MQ=255)

              aGGCAGATCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGCCCAATTTCTTCAcc                                                                                                                        >  1:816132/1‑143 (MQ=255)

               ggCAGATCACGTGATCGTGGTGATGTGGCTGGGTCAGTTCAAATACGGATTTAACGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACTCAGACCAATTTCTTCAccc                                                                                                                       <  1:615554/143‑1 (MQ=255)

                gCAGATCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCa                                                                                                                      >  1:365494/1‑143 (MQ=255)

                     tCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGAGTTACCGCCTTCAAAATGGTGGCGGGTGGCGATACCAGCGTCGTCAAACAGGTTCAGCACCCGCCATACCGTACCCAAACCACTTTCATCACCCATACCg                                                                                                                 >  2:59918/1‑143 (MQ=255)

                       aGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGAt                                                                                                               <  1:26009/143‑1 (MQ=255)

                        ggTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATc                                                                                                              <  2:131768/143‑1 (MQ=255)

                            aTCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCCGAc                                                                                                          >  2:756126/1‑143 (MQ=255)

                              cGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGt                                                                                                        <  1:42443/143‑1 (MQ=255)

                              cGTGGCGATGTTGCTCTGTCAGTTCAAACACGGATTTACCGCTTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGt                                                                                                        <  1:36676/143‑1 (MQ=255)

                                      tGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATaa                                                                                                <  1:518779/143‑1 (MQ=255)

                                        ttGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATCTCGATCAGACGTTTGTATAAAt                                                                                              >  1:957391/1‑143 (MQ=255)

                                                tCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCCATATACCGTACCCCGACCAATTTCTTCACCCATATCGATCAGACGCTTGTACCAATCCTCCGCa                                                                                      >  2:834390/1‑143 (MQ=255)

                                                  aGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAGATATTCCGCACt                                                                                    >  2:847651/1‑143 (MQ=255)

                                                   gTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATCTACCGTACCCAGACCAATTTCTGCACCCATATCGAGCAGACGATTGTATAAATCTTCCGCACTg                                                                                   >  2:403511/1‑143 (MQ=255)

                                                   gTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTg                                                                                   >  1:823905/1‑143 (MQ=255)

                                                    ttCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGCTTGTATAAATCTTCCGCCCTGa                                                                                  >  1:496528/1‑143 (MQ=255)

                                                         aTACGGATTTACCGCCTTCAAAATTGTGGCGGGCGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGCCCAATTTCTTCACCCATATCGATCAGACGCCTGTAGCAATCTTCCCCACTGACGCGa                                                                             >  2:510466/1‑143 (MQ=255)

                                                           aCGGATTTACCGCCTTCATAATGGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATg                                                                           <  1:687194/143‑1 (MQ=255)

                                                           aCGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACAGTACCCAGACCAATGTCTTCCCCCATATCGATCATACGTTTGTACAAATTTTGCGCCCCAACgtggtg                                                                           >  2:928109/1‑143 (MQ=255)

                                                           aCGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACAAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATAGATCCGCCGTCTGTACAAATTTTCAGCACGGACGTGCTg                                                                           >  2:95221/1‑143 (MQ=255)

                                                             ggATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCCATTTCTTCCCCCATATCTATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATAGt                                                                         >  1:2573/1‑143 (MQ=255)

                                                                  tACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTcc                                                                    <  1:623005/143‑1 (MQ=255)

                                                                    cccccTTCAAAATTGTGGCGGGTGACGATACCCGCGTCGTCAAACTGGTTCAGCACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCgg                                                                  <  2:320248/140‑1 (MQ=255)

                                                                     cGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATAGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGc                                                                 >  2:616180/1‑143 (MQ=255)

                                                                         ttCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCt                                                             <  1:988497/143‑1 (MQ=255)

                                                                         tcccaaaTTGTGGCTGGTTCCGATATCAGTGTTGCTAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATCTCGATCAGACGTTTGTATAAATCTTCCGCTCTGACGTGATGGTTGTCCGGCTCCt                                                             <  2:709990/139‑1 (MQ=255)

                                                                                ttGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTCGTATGGGCCCTGAAAAAc                                                      >  2:766173/1‑143 (MQ=255)

                                                                                        ggTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCACTTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGa                                              >  2:370078/1‑143 (MQ=255)

                                                                                            aCGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGAtttt                                          >  1:1011683/1‑143 (MQ=255)

                                                                                                 aCCTGCGTCGTCAATCTTGTTCAGTACGCGTTATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGTCTCCTGAAGAACTTCCAGGATTTTTAAAc                                     <  2:584213/143‑1 (MQ=255)

                                                                                                   cAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACGTCCAGGATTTTTAAACGa                                   >  2:584670/1‑143 (MQ=255)

                                                                                                        tcgtcAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGAGATGGTTGTCCGGCTCCTGAAGAACATCCAGGATTTTTAAACGAGGAAg                              >  2:11108/1‑143 (MQ=255)

                                                                                                           tcAAACTGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGt                           >  1:858229/1‑143 (MQ=255)

                                                                                                                 tGGTTCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGAGTTTTACACGAGGAAGCGTTACttt                     >  2:234338/1‑143 (MQ=255)

                                                                                                                    ttCAGTACGCGATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAg                  <  1:769954/143‑1 (MQ=255)

                                                                                                                             cgATATACCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGcttt         <  1:259024/143‑1 (MQ=255)

                                                                                                                                tataCCGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGctttctt      <  1:616180/143‑1 (MQ=255)

                                                                                                                                  tgctgTAGGCAGATCAATTTCTTCACCCGTGGCGTTCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGCCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTa    <  2:653582/139‑1 (MQ=255)

                                                                                                                                    ccGTACCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAgg  >  1:352601/1‑143 (MQ=255)

CCTTGCCGCAGTCGAGGCAGATCAGGTGATCGTGGTGATGTTGCTGTGTCAGTTCAAATACGGATTTACCGCCTTCAAAATTGTGGCGGGTGACGATACCAGCGTCGTCAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGG  >  NC_000913/710352‑710626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A