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
A20 F4 I5 R1	61	40.1	2005705	98.2%	1969602	131.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AE015451_phaM1	5,674,751	+G	intergenic (+113/+27)	rhlE‑II CDS (ATP‑dependent RNA helicase) → / ← yceI CDS (polyisoprene‑binding protein_ acidic stress response factor)	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451_phaM1	5,674,750	1	.	G	100.0%	115.9 / NA	32	intergenic (+112/+28)	rhlE‑II CDS (ATP‑dependent RNA helicase)/yceI CDS (polyisoprene‑binding protein_ acidic stress response factor)	–/–
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (15/17); total (15/17)

GCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCG  >  AE015451_phaM1/5674634‑5674883

gttggtggAAGTACCTGGGGGGCTGCTTCGCAGCCCCATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTGGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGaa                                                                                                             <  2:592269/137‑1 (MQ=37)

gcggagaGAAGTACCGGGGGGGCTGCTTCGCATCCCTATCACAACACAGGGCCTCTCCGAAAGAGAATTTCTTGACCTCTACAGGAGTGGCTTTTTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGTTTTTCAGCTGGCAGaa                                                                                                             <  2:224072/138‑1 (MQ=255)

         aGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTc                                                                                                     <  6:4323/143‑1 (MQ=255)

             ccGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAACGGCCCCCTCGGTTTTCGGCTGGCAGAAATTACTTCTGCtt                                                                                                >  1:170873/1‑144 (MQ=38)

                           tCGCAGCCCTGGCACGATATAAGGCCGCTCCTGCAGAGAGTTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCCGGCAGAAATTACTTCTGCTTCACAACTTCGaca                                                                                   <  6:49898/143‑1 (MQ=37)

                           tCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGacac                                                                                  >  2:372816/1‑144 (MQ=255)

                            cGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCg                                                                                      <  6:109912/139‑1 (MQ=255)

                            cGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCg                                                                                      >  5:109912/1‑139 (MQ=255)

                                    tATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCACTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtcc                                                                          >  6:74051/1‑143 (MQ=255)

                                      tCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGtttt                                                                                                                         >  3:91689/1‑94 (MQ=37)

                                           acacAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCAGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCACCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATAtccaggtcca                                                                   >  6:84889/1‑143 (MQ=255)

                                             acaAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTgg                                                                                                                  <  4:85756/94‑1 (MQ=37)

                                              caAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGt                                                               >  1:448617/1‑144 (MQ=255)

                                                aGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAg                                                                                                               <  3:47861/94‑1 (MQ=37)

                                                      cTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAg                                                       >  1:182070/1‑144 (MQ=255)

                                                      cTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAg                                                       >  1:182071/1‑144 (MQ=255)

                                                      cTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAg                                                       <  2:182070/144‑1 (MQ=255)

                                                      cTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAg                                                       <  2:182071/144‑1 (MQ=255)

                                                               agaATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCtt                                                                                                >  4:50773/1‑94 (MQ=37)

                                                                gaATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCgg                                             <  2:90628/144‑1 (MQ=255)

                                                                gaATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCgg                                             <  2:90630/144‑1 (MQ=255)

                                                                gaATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCgg                                             <  2:90629/144‑1 (MQ=255)

                                                                aaaTTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCgg                                             <  2:632086/143‑1 (MQ=255)

                                                                   tttCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGc                                           >  5:15688/1‑143 (MQ=255)

                                                                                aCAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAg                             >  2:31304/1‑144 (MQ=255)

                                                                                aCAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAg                             >  2:87020/1‑144 (MQ=255)

                                                                                               tgtCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGc              >  2:559058/1‑144 (MQ=255)

                                                                                                       tAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCgtggtggt      <  2:429672/144‑1 (MQ=255)

                                                                                                           gCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCg  <  1:31304/144‑1 (MQ=255)

                                                                                                           gCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTGCAGCGTGGTGGTGGCg  <  1:87020/144‑1 (MQ=255)

                                                                                                            ccGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGt                                                      <  3:61504/91‑1 (MQ=255)

                                                                                                            ccGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGt                                                      >  4:61504/1‑91 (MQ=255)

GCTGATAGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCG  >  AE015451_phaM1/5674634‑5674883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGC  >  AE015451_phaM1/5674640‑5674890

AGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAACGGCCCCCTCGGTTTTCGGCTGGCAGAAATTACTTCTGCTT                                                                                                       >  LH00444:58:22357VLT4:2:1327:48194:9461/1‑151 (MQ=60)

              GGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACAC                                                                                         >  LH00444:90:22JGJLLT3:8:2248:9673:29295/1‑151 (MQ=60)

                         AGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTT                                                                                                                                >  LH00444:62:22GH52LT3:8:1254:12613:24617/1‑101 (MQ=60)

                                 CACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGT                                                                      >  LH00444:58:22357VLT4:2:2271:2845:14139/1‑151 (MQ=60)

                                         AAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAG                                                              >  LH00444:58:22357VLT4:2:1341:47838:19882/1‑151 (MQ=60)

                                         AAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAG                                                              >  LH00444:58:22357VLT4:2:1341:47846:19896/1‑151 (MQ=60)

                                          AGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTAC                                                                                                               <  LH00444:62:22GH52LT3:8:1178:18586:14619/101‑1 (MQ=60)

                                                     GCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGC                                                  >  LH00444:90:22JGJLLT3:8:1128:39103:9155/1‑151 (MQ=60)

                                                              TTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATCTCCAGGTCCAGGGTCTGCGAAGTAGTACCCGGGCCTTTGATGC                                         >  LH00444:90:22JGJLLT3:8:1108:6095:5951/1‑151 (MQ=60)

                                                                                                   GGGCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCC                                                      <  LH00444:62:22GH52LT3:8:1203:14370:8691/101‑1 (MQ=60)

                                                                                                     GCCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGC  <  LH00444:58:22357VLT4:2:1143:45677:1854/151‑1 (MQ=60)

                                                                                                     ACCGCAAAGCGGCCCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGGCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTGCAGCGTGGTGGTGGCGgggaaga  <  LH00444:58:22357VLT4:2:1214:1712:25261/151‑8 (MQ=60)

AGAAGTACCGAGGGGGCTGCTTCGCAGCCCTATCACGACACAAGGCCGCTCCTGCAGAGAATTTCTTGATCTCTACAGGAGCGGCCTTGTGTCGTGATAGGGCCGCAAAGC‑GCGCCCTCGGTTTTCAGCTGGCAGAAATTACTTCTGCTTCACACCTTCGACACTGATATCCAGGTCCAGGGTCTGCGAAGTAGCACCCGGGCCTTTGATGCCGAAGTCGTTCAGGTTCAGCGTGGTGGTGGCGTTGAAGC  >  AE015451_phaM1/5674640‑5674890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`