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
A7 F28 I1 R1	252	48.5	1661298	98.8%	1641362	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,958,104	(T)_6→7	coding (781/2889 nt)	ptrA ←	protease 3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,958,098	1	.	T	97.6%	141.5 / ‑3.6	42	coding (787/2889 nt)	ptrA	protease 3
Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (22/19); total (22/20)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCATCGGTTTTACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑TTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGAATAGTACTTCTCGTGG  >  NC_000913/2957959‑2958222

tCATCGGTTTTACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCgg                                                                                                                               >  1:180504/1‑140 (MQ=255)

       ttttACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑ttttttt                                                                                                                       >  2:803673/1‑139 (MQ=255)

        tttACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑tttttttg                                                                                                                      <  1:803673/140‑3 (MQ=255)

         ttACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑tttttttgc                                                                                                                     <  1:176551/140‑4 (MQ=255)

                   aCTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGtt                                                                                                            <  1:524948/140‑1 (MQ=255)

                    cTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGctct                                                                                                                   >  1:363247/1‑132 (MQ=255)

                    cTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGctct                                                                                                                   <  2:363247/132‑1 (MQ=255)

                    cTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTc                                                                                                           >  1:639398/1‑140 (MQ=255)

                       cGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGc                                                                                                        >  1:294310/1‑140 (MQ=255)

                       cGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑tttttttgc                                                                                                                     >  2:635990/1‑123 (MQ=255)

                       cGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑tttttttgc                                                                                                                     <  1:635990/126‑4 (MQ=255)

                         cTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCAc                                                                                                      <  2:467937/140‑1 (MQ=255)

                         cTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCAc                                                                                                      >  1:310526/1‑140 (MQ=255)

                         cTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCAc                                                                                                      <  1:198416/140‑1 (MQ=255)

                            aGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCAcgcg                                                                                                   >  1:638002/1‑140 (MQ=255)

                             gttgttATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGa                                                                                                  <  2:294310/140‑1 (MQ=255)

                                 ttATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCaa                                                                                              >  1:790908/1‑140 (MQ=255)

                                 ttATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCaa                                                                                              >  1:557419/1‑140 (MQ=255)

                                   aTCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAg                                                                                            >  1:499630/1‑140 (MQ=255)

                                     cGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGgt                                                                                          <  2:134737/140‑1 (MQ=255)

                                        tGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTc                                                                                       >  1:447302/1‑140 (MQ=255)

                                                       gcAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑TTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGcc                                                                       <  2:180504/140‑1 (MQ=255)

                                                                   gcgGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAg                                                            <  2:311593/140‑1 (MQ=255)

                                                                     ggCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCg                                                          <  2:92555/140‑1 (MQ=255)

                                                                     ggCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCg                                                          >  1:616541/1‑140 (MQ=255)

                                                                      gCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCgg                                                         >  2:146473/1‑140 (MQ=255)

                                                                       cAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGt                                                        >  2:802192/1‑140 (MQ=255)

                                                                       cAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGt                                                        >  2:315280/1‑140 (MQ=255)

                                                                        aGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGtt                                                       <  2:790908/140‑1 (MQ=255)

                                                                           gcAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTttat                                                    <  2:639398/140‑1 (MQ=255)

                                                                             aGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTttatta                                                  <  2:499630/140‑1 (MQ=255)

                                                                               ggACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACt                                                <  2:336625/140‑1 (MQ=255)

                                                                                    tAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACt                                                <  2:359171/135‑1 (MQ=255)

                                                                                    tAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACt                                                >  1:359171/1‑135 (MQ=255)

                                                                                         aatgaTAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGTTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAAcc                                      >  2:24699/1‑140 (MQ=255)

                                                                                                aTGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTtca                               >  2:309237/1‑140 (MQ=255)

                                                                                                 tGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTtcat                              >  1:337260/1‑140 (MQ=255)

                                                                                                   cccTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTtcatca                            >  1:492588/1‑140 (MQ=255)

                                                                                                   cccTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTtcatca                            >  2:568538/1‑140 (MQ=255)

                                                                                                      ttttGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAAt                         <  2:64004/140‑1 (MQ=255)

                                                                                                       tttGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAAtt                        >  2:299957/1‑140 (MQ=255)

                                                                                                        ttGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTg                       >  2:724823/1‑140 (MQ=255)

                                                                                                         tGCGCGTCGGTGACTACCGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTgg                      <  1:724823/140‑1 (MQ=255)

                                                                                                                          cGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGaa                 <  2:680161/128‑1 (MQ=255)

                                                                                                                          cGGCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGaa                 >  1:680161/1‑128 (MQ=255)

                                                                                                                           ggCACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGAATAGTACTTCTCGt    <  1:309237/140‑1 (MQ=255)

                                                                                                                             cACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGAATAGTACTTCTCGTgg  <  1:146473/140‑1 (MQ=255)

                                                                                                                             cACGGTGATTTCCGGTTTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGAATAGTACTTCTCGTgg  <  2:492588/140‑1 (MQ=255)

TCATCGGTTTTACTACGGAACTTCGCTGAGTTGTTATCGATGCGAAACTCAACGCGCAACACTTTACGCGGCAGCGCAGGGACGTAATGAATGATAATGCCCTTTTGCGCGTCGGTGACTACCGGCACGGTGATTTCCGG‑TTTTTTGCTCTCTTTGTTCGGCACGCGACCAAAGGTGTCCGCCGCCATTTTTGCCAACTCCGGCAGCGGTTTATTACTGTAAATAACCGCCTTCATCAAATTGGCGGAATAGTACTTCTCGTGG  >  NC_000913/2957959‑2958222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A