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 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	861,316	T→C	I169V (ATT→GTT)	moeA ←	molybdopterin molybdotransferase MoeA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	861,316	0	T	C	90.3%	85.5 / 3.0	31	I169V (ATT→GTT)	moeA	molybdopterin molybdotransferase MoeA
Reads supporting (aligned to +/- strand): ref base T (2/1); new base C (15/13); total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

ACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCA  >  NZ_CP009273/861184‑861450

aCATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAAcccc                                                                                                                                     <  1:705217/136‑1 (MQ=255)

aCATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAg                                                                                                                                  >  2:528030/1‑139 (MQ=255)

     aGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAg                                                                                                                             >  2:600752/1‑139 (MQ=255)

     aGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAg                                                                                                                             >  1:41485/1‑139 (MQ=255)

     aGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAg                                                                                                                             >  1:810035/1‑139 (MQ=255)

               cGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTgg                                                                                                                   <  1:67411/139‑1 (MQ=255)

                 agaCGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTgg                                                                                                                   >  2:843076/1‑137 (MQ=255)

                  gaCGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAg                                                                                                                >  1:233948/1‑139 (MQ=255)

                  gaCGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAg                                                                                                                <  1:600752/139‑1 (MQ=255)

                             tCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAg                                                                                                     <  1:743966/139‑1 (MQ=255)

                               gTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGt                                                                                                                                 <  1:255455/109‑1 (MQ=255)

                               gTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGt                                                                                                                                 >  2:255455/1‑109 (MQ=255)

                                    tttGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGc                                                                                               >  2:695101/1‑138 (MQ=255)

                                          cGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTcc                                                                                        >  2:174679/1‑139 (MQ=255)

                                                   gCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGaa                                                                               <  1:174679/139‑1 (MQ=255)

                                                      gCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCg                                                                                                         <  2:250246/110‑1 (MQ=255)

                                                      gCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCg                                                                                                         >  1:250246/1‑110 (MQ=255)

                                                                 aaCTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTg                                                                 <  2:389591/139‑1 (MQ=255)

                                                                 aaCTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTg                                                                 <  2:715828/139‑1 (MQ=255)

                                                                      gAGTTCATCACCGGTAGAAAAAGGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCaga                                                             <  2:205727/138‑1 (MQ=255)

                                                                         ttCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGata                                                         >  1:500191/1‑139 (MQ=255)

                                                                              caCCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTTGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCtt                                                     >  2:101477/1‑138 (MQ=255)

                                                                                  ggTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACcg                                                >  2:362551/1‑139 (MQ=255)

                                                                                    tAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACcgcg                                              <  1:695101/139‑1 (MQ=255)

                                                                                              cgcTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAg                                                                                                                >  1:783785/1‑63 (MQ=255)

                                                                                              cgcTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAg                                                                                                                <  2:783785/63‑1 (MQ=255)

                                                                                                 tACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATAttt                                 >  1:140145/1‑139 (MQ=255)

                                                                                                    acGCATTTGTCGAATACCCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGTGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGc                              <  2:864225/139‑1 (MQ=255)

                                                                                                                    aCCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTcag              <  1:362551/139‑1 (MQ=255)

                                                                                                                              cGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAacg    >  2:857865/1‑139 (MQ=255)

                                                                                                                                gCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAacgca  >  1:662134/1‑139 (MQ=255)

                                                                                                                                gCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAacgca  <  1:742453/139‑1 (MQ=255)

ACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCA  >  NZ_CP009273/861184‑861450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CATCCCAACTGTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCACGCCATTGTCC  >  NZ_CP009273/861168‑861461

CATCCCAACTGTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCC                                                                                                                                                 >  SRR3722120.395309/1‑151 (MQ=60)

       ACTGTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGA                                                                                                                                          <  SRR3722120.694099/151‑1 (MQ=60)

          GTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGC                                                                                                                                       >  SRR3722120.820944/1‑151 (MQ=60)

          GTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGC                                                                                                                                       >  SRR3722120.41986/1‑151 (MQ=60)

               AACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAA                                                                                                                                     <  SRR3722120.714824/148‑1 (MQ=60)

                gagatgtgtataagagacagCGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTAC                                                                                                                                 <  SRR3722120.259151/131‑1 (MQ=60)

                       GTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAGC                                                                                                                          >  SRR3722120.237264/1‑151 (MQ=60)

                              GCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGG                                                                                                                   <  SRR3722120.68298/151‑1 (MQ=60)

                                 AGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAG                                                                                                                <  SRR3722120.609101/151‑1 (MQ=60)

                                            ATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTT                                                                                                     <  SRR3722120.754039/151‑1 (MQ=60)

                                                           GTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGctgtctcttatacacatct                                                                                      >  SRR3722120.253878/1‑132 (MQ=60)

                                                                  AGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCAC                                                                               <  SRR3722120.177062/151‑1 (MQ=60)

                                                                              GGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATAT                                                                   >  SRR3722120.507366/1‑151 (MQ=60)

                                                                                                   GTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttg                                              >  SRR3722120.794340/1‑85 (MQ=60)

                                                                                                   GTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATAT                                              <  SRR3722120.704591/151‑1 (MQ=60)

                                                                                                      GAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTT                                           >  SRR3722120.142037/1‑151 (MQ=60)

                                                                                                                                   CACCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGC              <  SRR3722120.367826/151‑1 (MQ=60)

                                                                                                                                     CCGGAACTTCGGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCAC            >  SRR3722120.671213/1‑151 (MQ=60)

                                                                                                                                               GGCAACCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCACGCCATTGTCC  <  SRR3722120.752513/151‑1 (MQ=60)

CATCCCAACTGTTCTAACATCAGGTGTACGGCGAGACGGTTGGTATCGTAGATTTGGCCGTCGCCCAGCGGCTGACCGGGCAACTGGAGTTCATCACCGGTAGAAAAAAGCGCTACACGCACTTTACGAATCACCGGAACTTCGGCAATCCCCAGTGAAGCAATTACTGGCAGCTCTGCGGTAGTCAGGCGAGTTCCCGCCGGGAAAACAACCGCACCTGCAGAGATATCTTCACCGCGACGGCGAATATTTTGCCCGCTACGCACTTCAGCAGTAAAACGCACGCCATTGTCC  >  NZ_CP009273/861168‑861461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`