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 F1 I2 R1	77	34.8	1608548	95.0%	1528120	114.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,314,922	T→C	S479P (TCC→CCC)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,314,922	0	T	C	100.0%	101.6 / NA	27	S479P (TCC→CCC)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/15); total (12/15)

CATTATTCGCGATCAGGATCGCGAAGTGCTGGTAAACAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGA  >  NC_000913/2314786‑2315057

cATTATTCGCGATCAGGATCGCGAAGTGCTGGTAAACAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGccc                                                                                                                                       <  1:212030/139‑1 (MQ=255)

                gATCGCGAAGTGCTGGTAAACAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGCAAAACCAGCAGGGGCGGATGATCTTTATGCAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCgg                                                                                                                       <  1:527942/139‑1 (MQ=255)

                                                  aGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGc                                                                                     <  2:269963/139‑1 (MQ=255)

                                                              tGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGa                                                                         >  1:37785/1‑139 (MQ=255)

                                                                tATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGa                                                                         >  2:758700/1‑137 (MQ=255)

                                                                tATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGa                                                                         <  1:758700/137‑1 (MQ=255)

                                                                      aaaaaCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAgcg                                                                                                                          <  2:664626/82‑1 (MQ=255)

                                                                      aaaaaCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAgcg                                                                                                                          >  1:664626/1‑82 (MQ=255)

                                                                          aCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCg                                                             >  2:584003/1‑139 (MQ=255)

                                                                          aCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCg                                                             >  1:482188/1‑139 (MQ=255)

                                                                          aCCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCg                                                             >  2:268985/1‑139 (MQ=255)

                                                                          aCCAGCAGGGGCGGATAATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCg                                                             >  2:749177/1‑139 (MQ=255)

                                                                           ccAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCgg                                                            <  2:482188/139‑1 (MQ=255)

                                                                                agGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGt                                                       <  2:100044/139‑1 (MQ=255)

                                                                                    gCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTtgat                                                   <  1:268985/139‑1 (MQ=255)

                                                                                         tgatCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAATGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAAt                                              >  2:728170/1‑139 (MQ=255)

                                                                                              tttATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGt                                         >  1:205547/1‑139 (MQ=255)

                                                                                                  tGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGc                                     >  2:116893/1‑139 (MQ=255)

                                                                                                      aaaCATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAAc                                 <  1:736947/139‑1 (MQ=255)

                                                                                                      aaaCATTGGCGATGCGCTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAAc                                 >  2:736947/1‑139 (MQ=255)

                                                                                                                   gcgcTGAAAGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGgatg                    <  2:196223/139‑1 (MQ=255)

                                                                                                                          aaGAACCCGCACAGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTg             <  1:235549/139‑1 (MQ=255)

                                                                                                                                    acaGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGaaa                                               <  2:120985/95‑1 (MQ=255)

                                                                                                                                    acaGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGaaa                                               >  1:120985/1‑95 (MQ=255)

                                                                                                                                     caGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga  <  1:116893/139‑1 (MQ=255)

                                                                                                                                     caGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga  <  1:75919/139‑1 (MQ=255)

                                                                                                                                     caGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga  <  2:626759/139‑1 (MQ=255)

                                                                                                                                     caGCCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTAGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTgaga  <  1:749177/139‑1 (MQ=255)

CATTATTCGCGATCAGGATCGCGAAGTGCTGGTAAACAAGAAACTCAAGCAGGCGCAGCGTCTGTATGAGAAAAACCAGCAGGGGCGGATGATCTTTATGAAAAACATTGGCGATGCGCTGAAAGAACCCGCACAGTCCCTGGCGGAGAGCGCGGCTAAACTCAACGCCCCGGAAAGCAAACAACTGGCGAATCAGGCAGATGTGCTGGTGCGGCTGGTTGATGAAATACAGTTAGCGAACATGCTTGCGGATGATAGCTGGAAAAGTGAGA  >  NC_000913/2314786‑2315057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A