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
A14 F1 I2 R1	70	59.9	2639336	94.5%	2494172	113.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,845,226	G→A	P416S (CCA→TCA)	hycE ←	hydrogenase 3, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,845,226	0	G	A	93.8%	96.2 / ‑1.0	32	P416S (CCA→TCA)	hycE	hydrogenase 3, large subunit
Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (19/11); total (20/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

CTTCCACCATCAGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGGCAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAGACGACCAATGCCGACAGTGCGC  >  NC_000913/2845091‑2845359

cTTCCACCATCAGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGacag                                                                                                                                    <  2:733359/139‑1 (MQ=255)

   ccaccaTCAGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGAcagcag                                                                                                                                 >  2:408038/1‑139 (MQ=255)

         tCAGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATa                                                                                                                           >  1:734938/1‑139 (MQ=255)

           aGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGc                                                                                                                         >  2:119880/1‑139 (MQ=255)

                gCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACa                                                                                                                    <  1:598289/139‑1 (MQ=255)

                 ccACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACaa                                                                                                                   >  1:169490/1‑139 (MQ=255)

                     ccGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACgg                                                                                                               >  2:655070/1‑139 (MQ=255)

                          aGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGAt                                                                                                          <  2:169490/139‑1 (MQ=255)

                          aGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGAt                                                                                                          <  1:488681/139‑1 (MQ=255)

                                      ccGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTAt                                                                                              >  2:1309547/1‑139 (MQ=255)

                                         tAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCAc                                                                                           >  1:1150243/1‑139 (MQ=255)

                                          aGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACg                                                                                          >  1:1137382/1‑139 (MQ=255)

                                                   tGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAGCGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGAcc                                                                                 >  1:571240/1‑139 (MQ=255)

                                                          cgcgGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGGCAGCAGGCCATAGCCGACaaa                                                                                                                  >  1:784231/1‑99 (MQ=255)

                                                          cgcgGTAGAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGGCAGCAGGCCATAGCCGACaaa                                                                                                                  <  2:784231/99‑1 (MQ=255)

                                                                        cGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGcc                                                            >  2:634269/1‑139 (MQ=255)

                                                                         gTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACa                                                                                                                    <  1:534887/82‑1 (MQ=255)

                                                                         gTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACa                                                                                                                    >  2:534887/1‑82 (MQ=255)

                                                                         gTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCg                                                           >  1:589856/1‑139 (MQ=255)

                                                                         gTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCg                                                           >  1:101906/1‑139 (MQ=255)

                                                                                  cACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTg                                                  <  1:408038/139‑1 (MQ=255)

                                                                                     tttCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAg                                               >  1:916263/1‑139 (MQ=255)

                                                                                                     aCGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGa                                                                      >  2:1053897/1‑100 (MQ=255)

                                                                                                     aCGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGa                                                                      <  1:1053897/100‑1 (MQ=255)

                                                                                                         cGCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTc                           <  2:1137382/139‑1 (MQ=255)

                                                                                                          gCAGCCCTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTcc                          >  1:409953/1‑139 (MQ=255)

                                                                                                                cTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAgacga                    <  2:1019257/139‑1 (MQ=255)

                                                                                                                cTGCTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAgacga                    <  1:655070/139‑1 (MQ=255)

                                                                                                                   cTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGgcgc                                                                                                    >  1:489836/1‑56 (MQ=255)

                                                                                                                   cTCGCTGTGGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGgcgc                                                                                                    <  2:489836/56‑1 (MQ=255)

                                                                                                                        tgtgGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGc                                                             >  1:419750/1‑90 (MQ=255)

                                                                                                                        tgtgGACTTCCATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGc                                                             <  2:419750/90‑1 (MQ=255)

                                                                                                                                  cATTGACAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAGACGACCAATGCCGACAGTgcgc  >  1:311131/1‑139 (MQ=255)

CTTCCACCATCAGTGGGCCACCCGGCAGGTTATCCAGACCGTAGTCGATCATGTTCAGCGCGGTATAGACTTCGTTGATACGCACTTTCAGACGGGAAATAACGTCGCAGCCCTGCTCGCTGTGGACTTCCATTGGCAGCAGGCCATAGCCGACAAACGGGTGATCGGCGCGGGTATCACGGGCGTGACCGCTGGCACGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAGACGACCAATGCCGACAGTGCGC  >  NC_000913/2845091‑2845359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A