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
A1 F14 I0 R1	248	61.6	2601574	98.7%	2567753	146.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	5,677,565:1	+G	100%	intergenic (+112/+28)	rhlE‑II → / ← yceI	ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,677,565	1	.	G	100.0%	175.8 / NA	49	intergenic (+112/+28)	rhlE‑II/yceI	ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (23/26); total (23/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAAGGGCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGC  >  NC_002947_CJ‑RC/5677443‑5677705

gCAAGGGCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCGCGGTTTTCAgcaggcag                                                                                                                      >  3:222669/1‑148 (MQ=37)

      gCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTAc                                                                                                               <  6:76358/149‑1 (MQ=255)

      gCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTAc                                                                                                               >  2:25649/1‑149 (MQ=255)

          aTAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACtt                                                                                                             <  6:251316/147‑1 (MQ=255)

          aTAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTc                                                                                                            <  2:114021/148‑1 (MQ=255)

                   ccGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCacac                                                                                                  <  3:87773/149‑1 (MQ=255)

                      aGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCtt                                                                                               >  5:201442/1‑149 (MQ=255)

                       gggggCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTc                                                                                              <  2:256098/149‑1 (MQ=255)

                       gggggCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTc                                                                                              >  3:153303/1‑149 (MQ=255)

                           gctgctTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGaca                                                                                          >  1:13878/1‑149 (MQ=255)

                             tgctTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACt                                                                                        >  4:13700/1‑149 (MQ=255)

                             tgctTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACt                                                                                        >  2:127383/1‑149 (MQ=255)

                                    cAGCCCTATCACGACACACGGCCGCGCCTGAAGAGAATTTCTTGCTCTCAACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtcc                                                                                 <  4:5355/149‑1 (MQ=37)

                                    cAGCCCTATCACGACACAAGGCCGCTCCTCCAGAGAATTTCTTTAACTCTACAGGAGCGGCCTTGTGTCGTTATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtcc                                                                                 <  5:45875/149‑1 (MQ=38)

                                         cTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtccaggtc                                                                            <  1:127383/149‑1 (MQ=255)

                                              aCGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTGTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAggg                                                                       >  7:185235/1‑149 (MQ=255)

                                              aCGACACAAGGCCGCTCATGCAGATAATTTCTTGATCTCTACTGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtccaggtccagg                                                                        <  5:248915/148‑1 (MQ=39)

                                                  cacaAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTg                                                                   >  2:102338/1‑149 (MQ=255)

                                                     aaGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCg                                                                 >  6:229360/1‑148 (MQ=255)

                                                     aaGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCg                                                                 >  5:11731/1‑148 (MQ=255)

                                                     aaGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCg                                                                 >  5:16253/1‑148 (MQ=255)

                                                     aaGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCg                                                                 >  7:264654/1‑148 (MQ=255)

                                                      aGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGaa                                                               <  2:239936/149‑1 (MQ=255)

                                                      aGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGaa                                                               <  2:13878/149‑1 (MQ=255)

                                                       ggCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAg                                                              <  6:190114/149‑1 (MQ=255)

                                                         ccGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTa                                                            <  7:155247/149‑1 (MQ=255)

                                                          cGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAg                                                           <  2:98193/149‑1 (MQ=255)

                                                           gCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAg                                                           >  5:302984/1‑148 (MQ=255)

                                                                  cAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCggg                                                   >  2:120574/1‑149 (MQ=255)

                                                                  cAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTATCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGAGAAGTAGCACCCggg                                                   >  6:16045/1‑149 (MQ=39)

                                                                          ttCTTTATCTCTACAGGAGAGGCATTGTGTCGTGATATGGCCGCAAAGCGGCCCCCTGGGTTTTCAGCTGGGAGAAATTACTTCTTCTTCACACCTTCGACACTGATATCCAGGTCCAGTGTCTGCGAAGTAGCTCCCGGGCCTTTGa                                            <  7:158718/148‑1 (MQ=255)

                                                                           tCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGAt                                           <  1:4647/148‑1 (MQ=255)

                                                                           tCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATg                                          >  8:299867/1‑149 (MQ=255)

                                                                                     tACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAg                                    <  6:120192/145‑1 (MQ=255)

                                                                                       cAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCgttc                              <  4:258246/149‑1 (MQ=255)

                                                                                        aGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCgtt                               >  8:191900/1‑147 (MQ=255)

                                                                                          gAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTTCTTCTGCTTCCCACCTTCGACACTGATATACAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCgttcagg                           >  3:80400/1‑149 (MQ=39)

                                                                                               gCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCgttcaggttcag                      >  4:86422/1‑149 (MQ=255)

                                                                                                ccTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGc                     >  1:109343/1‑149 (MQ=255)

                                                                                                       tCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCgtggtg               <  1:25649/148‑1 (MQ=255)

                                                                                                         gTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCgtggtggtg            <  6:302984/149‑1 (MQ=255)

                                                                                                              aGGGCCGCAACGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGGCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGt        <  8:185235/148‑1 (MQ=255)

                                                                                                               gggCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGtt       <  6:98911/148‑1 (MQ=255)

                                                                                                                 gCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGaa    <  6:16253/149‑1 (MQ=255)

                                                                                                                 gCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGaa    <  6:11731/149‑1 (MQ=255)

                                                                                                                 gCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGaa    <  4:58902/149‑1 (MQ=255)

                                                                                                                   cGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGt                                                             <  2:299838/90‑1 (MQ=255)

                                                                                                                   cGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGt                                                             >  1:299838/1‑90 (MQ=255)

                                                                                                                    gCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGc  >  6:318396/1‑148 (MQ=255)

GCAAGGGCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGC  >  NC_002947_CJ‑RC/5677443‑5677705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A